Starting phenix.real_space_refine on Wed Sep 17 20:53:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ysz_39566/09_2025/8ysz_39566.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ysz_39566/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ysz_39566/09_2025/8ysz_39566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ysz_39566/09_2025/8ysz_39566.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ysz_39566/09_2025/8ysz_39566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ysz_39566/09_2025/8ysz_39566.map" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.08, per 1000 atoms: 0.28 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: 1.07 Conformation dependent library (CDL) restraints added in 476.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.38 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: 2.10 Time building geometry restraints manager: 1.43 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: 0.000 Normalize map: mean=0, sd=1: 11.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.670 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.710 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.004 0.000 ARG B 604 TYR 0.010 0.001 TYR A 606 PHE 0.009 0.001 PHE E 19 TRP 0.010 0.001 TRP A 556 HIS 0.007 0.001 HIS A 892 Details of bonding type rmsd covalent geometry : bond 0.00300 (11417) covalent geometry : angle 0.65805 (15443) SS BOND : bond 0.00263 ( 24) SS BOND : angle 0.79591 ( 48) hydrogen bonds : bond 0.23438 ( 243) hydrogen bonds : angle 9.77880 ( 648) *********************** 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 : 0.474 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: 0.1129 time to fit residues: 12.9739 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 : 0.487 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.0060 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.5402 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.085101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.058851 restraints weight = 44764.507| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 4.32 r_work: 0.3031 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 11441 Z= 0.251 Angle : 0.712 11.179 15491 Z= 0.371 Chirality : 0.046 0.175 1682 Planarity : 0.004 0.030 1991 Dihedral : 5.964 23.997 1506 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.76 % Favored : 91.17 % Rotamer: Outliers : 2.25 % Allowed : 12.76 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.22), residues: 1336 helix: -0.83 (0.40), residues: 160 sheet: -1.46 (0.31), residues: 265 loop : -1.14 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 49 TYR 0.017 0.002 TYR A 428 PHE 0.014 0.002 PHE A 454 TRP 0.015 0.002 TRP A 439 HIS 0.009 0.001 HIS A 654 Details of bonding type rmsd covalent geometry : bond 0.00565 (11417) covalent geometry : angle 0.71150 (15443) SS BOND : bond 0.00359 ( 24) SS BOND : angle 0.96047 ( 48) hydrogen bonds : bond 0.05253 ( 243) hydrogen bonds : angle 7.47423 ( 648) *********************** 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 90 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 62 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 LEU cc_start: 0.9404 (pp) cc_final: 0.9123 (mp) REVERT: A 431 ASP cc_start: 0.8387 (t0) cc_final: 0.8075 (t0) REVERT: A 601 ASP cc_start: 0.8853 (p0) cc_final: 0.8296 (t0) REVERT: B 892 HIS cc_start: 0.9374 (OUTLIER) cc_final: 0.8990 (t-170) REVERT: C 17 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8493 (tt) outliers start: 28 outliers final: 11 residues processed: 85 average time/residue: 0.0868 time to fit residues: 11.9532 Evaluate side-chains 65 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 579 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 496 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 531 MET 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 15 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 103 optimal weight: 0.0170 chunk 26 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 73 optimal weight: 0.0670 chunk 11 optimal weight: 0.8980 overall best weight: 0.3956 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.086795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.060771 restraints weight = 44844.727| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 4.37 r_work: 0.3087 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11441 Z= 0.108 Angle : 0.612 9.929 15491 Z= 0.316 Chirality : 0.043 0.147 1682 Planarity : 0.003 0.031 1991 Dihedral : 5.470 22.706 1502 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.81 % Favored : 93.11 % Rotamer: Outliers : 2.01 % Allowed : 14.29 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.23), residues: 1336 helix: -0.55 (0.41), residues: 160 sheet: -1.25 (0.32), residues: 243 loop : -1.09 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 897 TYR 0.012 0.001 TYR B 876 PHE 0.015 0.001 PHE A 258 TRP 0.020 0.001 TRP A 924 HIS 0.010 0.001 HIS A 654 Details of bonding type rmsd covalent geometry : bond 0.00228 (11417) covalent geometry : angle 0.61180 (15443) SS BOND : bond 0.00244 ( 24) SS BOND : angle 0.76766 ( 48) hydrogen bonds : bond 0.04211 ( 243) hydrogen bonds : angle 6.83146 ( 648) *********************** 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 91 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 LEU cc_start: 0.9388 (pp) cc_final: 0.9114 (mp) REVERT: A 277 ASP cc_start: 0.8656 (t0) cc_final: 0.8226 (t0) REVERT: A 431 ASP cc_start: 0.8363 (t0) cc_final: 0.8030 (t0) REVERT: A 601 ASP cc_start: 0.8809 (p0) cc_final: 0.8305 (t0) REVERT: A 856 HIS cc_start: 0.9335 (OUTLIER) cc_final: 0.9128 (t-90) REVERT: A 858 MET cc_start: 0.8122 (mpp) cc_final: 0.7289 (mpp) REVERT: B 382 GLU cc_start: 0.8578 (tp30) cc_final: 0.8051 (mm-30) REVERT: B 446 LEU cc_start: 0.7421 (mt) cc_final: 0.7167 (mt) REVERT: B 469 MET cc_start: 0.8352 (tpt) cc_final: 0.8056 (tpt) REVERT: B 543 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8173 (m) REVERT: B 892 HIS cc_start: 0.9351 (OUTLIER) cc_final: 0.9090 (t-170) outliers start: 25 outliers final: 10 residues processed: 87 average time/residue: 0.0965 time to fit residues: 13.0846 Evaluate side-chains 71 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 579 LEU Chi-restraints excluded: chain A residue 856 HIS Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 543 THR 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 67 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 112 optimal weight: 0.3980 chunk 110 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 chunk 61 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 458 ASN ** B 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.086864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.060616 restraints weight = 45679.698| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 4.40 r_work: 0.3118 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11441 Z= 0.108 Angle : 0.577 9.535 15491 Z= 0.299 Chirality : 0.043 0.156 1682 Planarity : 0.003 0.043 1991 Dihedral : 5.197 21.157 1502 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.89 % Favored : 93.04 % Rotamer: Outliers : 1.85 % Allowed : 14.53 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.22), residues: 1336 helix: -0.75 (0.39), residues: 173 sheet: -1.19 (0.32), residues: 260 loop : -1.12 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 603 TYR 0.008 0.001 TYR A 606 PHE 0.015 0.001 PHE B 409 TRP 0.029 0.001 TRP A 924 HIS 0.010 0.001 HIS A 654 Details of bonding type rmsd covalent geometry : bond 0.00238 (11417) covalent geometry : angle 0.57674 (15443) SS BOND : bond 0.00138 ( 24) SS BOND : angle 0.69609 ( 48) hydrogen bonds : bond 0.03792 ( 243) hydrogen bonds : angle 6.52981 ( 648) *********************** 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 85 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 13 LEU cc_start: 0.9367 (pp) cc_final: 0.9053 (mp) REVERT: A 277 ASP cc_start: 0.8618 (t0) cc_final: 0.8207 (t0) REVERT: A 431 ASP cc_start: 0.8308 (t0) cc_final: 0.7986 (t0) REVERT: A 534 TYR cc_start: 0.8318 (p90) cc_final: 0.8101 (p90) REVERT: A 601 ASP cc_start: 0.8704 (p0) cc_final: 0.8232 (t0) REVERT: A 629 ILE cc_start: 0.9166 (mm) cc_final: 0.8847 (pt) REVERT: A 858 MET cc_start: 0.8104 (mpp) cc_final: 0.7640 (mpp) REVERT: B 382 GLU cc_start: 0.8521 (tp30) cc_final: 0.8040 (mm-30) outliers start: 23 outliers final: 12 residues processed: 81 average time/residue: 0.0881 time to fit residues: 11.5419 Evaluate side-chains 66 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 916 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 458 ASN 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 51 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.085935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.059721 restraints weight = 45332.519| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 4.37 r_work: 0.3092 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 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 : 0.004 0.032 11441 Z= 0.160 Angle : 0.582 8.904 15491 Z= 0.303 Chirality : 0.043 0.163 1682 Planarity : 0.003 0.037 1991 Dihedral : 5.170 20.690 1502 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.63 % Favored : 92.29 % Rotamer: Outliers : 2.09 % Allowed : 14.69 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.22), residues: 1336 helix: -0.78 (0.39), residues: 180 sheet: -1.19 (0.32), residues: 265 loop : -1.17 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 897 TYR 0.011 0.001 TYR A 428 PHE 0.013 0.001 PHE B 409 TRP 0.012 0.001 TRP A 859 HIS 0.011 0.001 HIS A 856 Details of bonding type rmsd covalent geometry : bond 0.00365 (11417) covalent geometry : angle 0.58136 (15443) SS BOND : bond 0.00232 ( 24) SS BOND : angle 0.68809 ( 48) hydrogen bonds : bond 0.03832 ( 243) hydrogen bonds : angle 6.45176 ( 648) *********************** 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 82 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 13 LEU cc_start: 0.9358 (pp) cc_final: 0.9017 (mp) REVERT: A 277 ASP cc_start: 0.8663 (t0) cc_final: 0.8225 (t0) REVERT: A 431 ASP cc_start: 0.8328 (t0) cc_final: 0.8036 (t0) REVERT: A 534 TYR cc_start: 0.8373 (p90) cc_final: 0.8163 (p90) REVERT: A 601 ASP cc_start: 0.8718 (p0) cc_final: 0.8214 (t0) REVERT: A 629 ILE cc_start: 0.9113 (mm) cc_final: 0.8806 (pt) outliers start: 26 outliers final: 16 residues processed: 79 average time/residue: 0.0692 time to fit residues: 9.1641 Evaluate side-chains 70 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 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 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 639 ILE Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain B residue 857 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 47 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN B 432 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.083424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.057199 restraints weight = 46155.462| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 4.24 r_work: 0.3021 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 11441 Z= 0.337 Angle : 0.728 10.668 15491 Z= 0.376 Chirality : 0.047 0.187 1682 Planarity : 0.004 0.054 1991 Dihedral : 5.752 20.249 1502 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.73 % Favored : 90.19 % Rotamer: Outliers : 2.81 % Allowed : 14.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.22), residues: 1336 helix: -0.75 (0.40), residues: 167 sheet: -1.64 (0.31), residues: 276 loop : -1.24 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 912 TYR 0.021 0.002 TYR A 428 PHE 0.020 0.002 PHE A 408 TRP 0.039 0.002 TRP A 924 HIS 0.014 0.001 HIS A 856 Details of bonding type rmsd covalent geometry : bond 0.00770 (11417) covalent geometry : angle 0.72727 (15443) SS BOND : bond 0.00485 ( 24) SS BOND : angle 0.95716 ( 48) hydrogen bonds : bond 0.04702 ( 243) hydrogen bonds : angle 6.80225 ( 648) *********************** 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 90 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 55 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8014 (pm20) REVERT: A 431 ASP cc_start: 0.8367 (t0) cc_final: 0.8094 (t0) REVERT: A 601 ASP cc_start: 0.8732 (p0) cc_final: 0.8170 (t0) REVERT: B 800 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7602 (pp) outliers start: 35 outliers final: 24 residues processed: 86 average time/residue: 0.0873 time to fit residues: 11.9385 Evaluate side-chains 75 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 49 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 51 GLU 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 489 ASN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 514 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 60 optimal weight: 4.9990 chunk 23 optimal weight: 0.0030 chunk 27 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 chunk 131 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.085619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.059654 restraints weight = 45207.020| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 4.26 r_work: 0.3100 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 11441 Z= 0.110 Angle : 0.585 8.584 15491 Z= 0.305 Chirality : 0.043 0.170 1682 Planarity : 0.003 0.036 1991 Dihedral : 5.289 19.902 1502 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.81 % Favored : 93.11 % Rotamer: Outliers : 2.09 % Allowed : 15.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.23), residues: 1336 helix: -0.47 (0.41), residues: 167 sheet: -1.36 (0.32), residues: 251 loop : -1.14 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 897 TYR 0.012 0.001 TYR C 59 PHE 0.017 0.001 PHE B 409 TRP 0.023 0.002 TRP A 924 HIS 0.010 0.001 HIS A 654 Details of bonding type rmsd covalent geometry : bond 0.00239 (11417) covalent geometry : angle 0.58369 (15443) SS BOND : bond 0.00172 ( 24) SS BOND : angle 0.97775 ( 48) hydrogen bonds : bond 0.03679 ( 243) hydrogen bonds : angle 6.41115 ( 648) *********************** 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 86 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 321 MET cc_start: 0.8456 (pmm) cc_final: 0.8111 (pmm) REVERT: A 431 ASP cc_start: 0.8270 (t0) cc_final: 0.8034 (t0) REVERT: A 601 ASP cc_start: 0.8653 (p0) cc_final: 0.8176 (t0) REVERT: A 833 MET cc_start: 0.6601 (OUTLIER) cc_final: 0.6170 (pmm) outliers start: 26 outliers final: 17 residues processed: 84 average time/residue: 0.0909 time to fit residues: 12.0095 Evaluate side-chains 71 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 403 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 514 LEU 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 19 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.084364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.058238 restraints weight = 45680.287| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 4.28 r_work: 0.3064 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11441 Z= 0.204 Angle : 0.628 10.185 15491 Z= 0.326 Chirality : 0.044 0.162 1682 Planarity : 0.004 0.077 1991 Dihedral : 5.334 19.659 1502 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.46 % Favored : 91.47 % Rotamer: Outliers : 2.73 % Allowed : 15.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.23), residues: 1336 helix: -0.45 (0.41), residues: 165 sheet: -1.53 (0.31), residues: 277 loop : -1.15 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 912 TYR 0.015 0.001 TYR A 428 PHE 0.018 0.002 PHE B 509 TRP 0.085 0.002 TRP A 924 HIS 0.010 0.001 HIS A 654 Details of bonding type rmsd covalent geometry : bond 0.00468 (11417) covalent geometry : angle 0.62657 (15443) SS BOND : bond 0.00327 ( 24) SS BOND : angle 0.91460 ( 48) hydrogen bonds : bond 0.03904 ( 243) hydrogen bonds : angle 6.47632 ( 648) *********************** 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 87 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 53 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 431 ASP cc_start: 0.8324 (t0) cc_final: 0.8045 (t0) REVERT: A 601 ASP cc_start: 0.8736 (p0) cc_final: 0.8196 (t0) REVERT: A 897 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.7110 (tmm-80) REVERT: B 800 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7534 (pp) outliers start: 34 outliers final: 23 residues processed: 83 average time/residue: 0.0801 time to fit residues: 10.8523 Evaluate side-chains 76 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 51 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 LEU 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 652 ILE Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 893 PHE Chi-restraints excluded: chain A residue 897 ARG Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 489 ASN 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 832 THR Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain B residue 857 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 119 optimal weight: 0.5980 chunk 87 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 66 optimal weight: 0.0980 chunk 112 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.085575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.059760 restraints weight = 44978.796| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 4.27 r_work: 0.3096 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11441 Z= 0.114 Angle : 0.599 10.064 15491 Z= 0.310 Chirality : 0.044 0.186 1682 Planarity : 0.004 0.096 1991 Dihedral : 5.212 24.427 1502 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.66 % Favored : 93.26 % Rotamer: Outliers : 2.01 % Allowed : 16.21 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.23), residues: 1336 helix: -0.33 (0.41), residues: 165 sheet: -1.31 (0.32), residues: 258 loop : -1.15 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG A 912 TYR 0.010 0.001 TYR A 87 PHE 0.013 0.001 PHE A 258 TRP 0.013 0.001 TRP A 859 HIS 0.011 0.001 HIS A 654 Details of bonding type rmsd covalent geometry : bond 0.00251 (11417) covalent geometry : angle 0.59862 (15443) SS BOND : bond 0.00157 ( 24) SS BOND : angle 0.80247 ( 48) hydrogen bonds : bond 0.03509 ( 243) hydrogen bonds : angle 6.26548 ( 648) *********************** 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: 25 poor density : 60 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 321 MET cc_start: 0.8496 (pmm) cc_final: 0.8147 (pmm) REVERT: A 431 ASP cc_start: 0.8282 (t0) cc_final: 0.8020 (t0) REVERT: A 601 ASP cc_start: 0.8675 (p0) cc_final: 0.8204 (t0) REVERT: A 897 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.7028 (tpp-160) REVERT: B 800 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7525 (pp) outliers start: 25 outliers final: 20 residues processed: 81 average time/residue: 0.0795 time to fit residues: 10.5387 Evaluate side-chains 79 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 LEU 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 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 884 LEU Chi-restraints excluded: chain A residue 893 PHE Chi-restraints excluded: chain A residue 897 ARG Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 453 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 Chi-restraints excluded: chain B residue 857 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 66 optimal weight: 0.0870 chunk 78 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 133 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 89 optimal weight: 0.0980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.085927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.059945 restraints weight = 45592.113| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 4.34 r_work: 0.3103 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3063 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= 0.105 Angle : 0.580 9.706 15491 Z= 0.299 Chirality : 0.043 0.187 1682 Planarity : 0.004 0.056 1991 Dihedral : 5.056 20.214 1502 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.04 % Favored : 92.89 % Rotamer: Outliers : 1.85 % Allowed : 16.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.23), residues: 1336 helix: -0.25 (0.41), residues: 165 sheet: -1.24 (0.31), residues: 268 loop : -1.17 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 912 TYR 0.014 0.001 TYR B 534 PHE 0.013 0.001 PHE A 258 TRP 0.011 0.001 TRP A 859 HIS 0.011 0.001 HIS A 654 Details of bonding type rmsd covalent geometry : bond 0.00231 (11417) covalent geometry : angle 0.57943 (15443) SS BOND : bond 0.00150 ( 24) SS BOND : angle 0.73369 ( 48) hydrogen bonds : bond 0.03418 ( 243) hydrogen bonds : angle 6.17702 ( 648) ********************** 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 84 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 321 MET cc_start: 0.8436 (pmm) cc_final: 0.8096 (pmm) REVERT: A 431 ASP cc_start: 0.8296 (t0) cc_final: 0.8035 (t0) REVERT: A 601 ASP cc_start: 0.8654 (p0) cc_final: 0.8198 (t0) REVERT: A 897 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.7079 (tpp-160) REVERT: B 800 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7474 (pp) outliers start: 23 outliers final: 21 residues processed: 81 average time/residue: 0.0856 time to fit residues: 11.2584 Evaluate side-chains 80 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 LEU 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 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 884 LEU Chi-restraints excluded: chain A residue 893 PHE Chi-restraints excluded: chain A residue 897 ARG Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 453 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 113 optimal weight: 7.9990 chunk 10 optimal weight: 0.0070 chunk 94 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 52 optimal weight: 0.4980 chunk 123 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.1004 ------------------------------------------------------------------------------- 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 = 0.3919 r_free = 0.3919 target = 0.085634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.059670 restraints weight = 45652.465| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 4.34 r_work: 0.3094 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3108 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= 0.128 Angle : 0.583 9.446 15491 Z= 0.301 Chirality : 0.043 0.174 1682 Planarity : 0.004 0.046 1991 Dihedral : 5.027 21.415 1502 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.19 % Favored : 92.74 % Rotamer: Outliers : 2.33 % Allowed : 16.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.23), residues: 1336 helix: -0.22 (0.41), residues: 165 sheet: -1.26 (0.32), residues: 267 loop : -1.15 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 912 TYR 0.012 0.001 TYR B 534 PHE 0.014 0.001 PHE B 509 TRP 0.010 0.001 TRP A 859 HIS 0.010 0.001 HIS A 654 Details of bonding type rmsd covalent geometry : bond 0.00292 (11417) covalent geometry : angle 0.58261 (15443) SS BOND : bond 0.00192 ( 24) SS BOND : angle 0.71437 ( 48) hydrogen bonds : bond 0.03475 ( 243) hydrogen bonds : angle 6.16595 ( 648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3869.58 seconds wall clock time: 66 minutes 49.05 seconds (4009.05 seconds total)