Starting phenix.real_space_refine on Fri Jul 3 07:17:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wjn_32546/07_2026/7wjn_32546.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wjn_32546/07_2026/7wjn_32546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wjn_32546/07_2026/7wjn_32546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wjn_32546/07_2026/7wjn_32546.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wjn_32546/07_2026/7wjn_32546.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wjn_32546/07_2026/7wjn_32546.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wjn_32546/07_2026/7wjn_32546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wjn_32546/07_2026/7wjn_32546.map" } resolution = 3.3 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 ------------------------------------------------------------------------------- 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= 0.003 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: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 P 4 5.49 5 S 74 5.16 5 C 8458 2.51 5 N 2170 2.21 5 O 2346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13054 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 6487 Classifications: {'peptide': 808} Link IDs: {'PTRANS': 30, 'TRANS': 777} Chain breaks: 2 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MN': 1, 'UD1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 6.65, per 1000 atoms: 0.51 Number of scatterers: 13054 At special positions: 0 Unit cell: (118.77, 112.35, 127.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 74 16.00 P 4 15.00 O 2346 8.00 N 2170 7.00 C 8458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 577.9 milliseconds 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3040 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 4 sheets defined 66.8% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 23 through 37 Processing helix chain 'A' and resid 66 through 74 removed outlier: 3.835A pdb=" N ASP A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 89 removed outlier: 3.764A pdb=" N SER A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 110 Processing helix chain 'A' and resid 112 through 134 removed outlier: 4.146A pdb=" N GLU A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ARG A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 163 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 221 through 227 Processing helix chain 'A' and resid 242 through 262 removed outlier: 3.940A pdb=" N LEU A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 282 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 311 through 319 Processing helix chain 'A' and resid 357 through 374 Processing helix chain 'A' and resid 390 through 403 removed outlier: 3.560A pdb=" N HIS A 403 " --> pdb=" O PHE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 447 removed outlier: 3.562A pdb=" N SER A 427 " --> pdb=" O ASN A 423 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 479 removed outlier: 5.156A pdb=" N THR A 476 " --> pdb=" O ALA A 472 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU A 477 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.666A pdb=" N LEU A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 493 removed outlier: 3.695A pdb=" N GLY A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 505 Processing helix chain 'A' and resid 528 through 554 Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 564 through 587 removed outlier: 3.650A pdb=" N PHE A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 605 Processing helix chain 'A' and resid 621 through 646 removed outlier: 4.235A pdb=" N VAL A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 681 Processing helix chain 'A' and resid 684 through 706 removed outlier: 5.302A pdb=" N VAL A 697 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N TYR A 698 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE A 699 " --> pdb=" O VAL A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 720 removed outlier: 5.368A pdb=" N THR A 716 " --> pdb=" O PHE A 712 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N HIS A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 735 Processing helix chain 'A' and resid 764 through 819 removed outlier: 3.581A pdb=" N PHE A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 853 Processing helix chain 'A' and resid 854 through 858 removed outlier: 3.779A pdb=" N GLY A 857 " --> pdb=" O GLY A 854 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ARG A 858 " --> pdb=" O LEU A 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 854 through 858' Processing helix chain 'B' and resid 24 through 37 Processing helix chain 'B' and resid 66 through 74 removed outlier: 3.835A pdb=" N ASP B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 89 removed outlier: 3.763A pdb=" N SER B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 110 Processing helix chain 'B' and resid 112 through 134 removed outlier: 4.145A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 163 Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 242 through 262 removed outlier: 3.941A pdb=" N LEU B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 282 Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 311 through 319 Processing helix chain 'B' and resid 357 through 374 Processing helix chain 'B' and resid 390 through 403 removed outlier: 3.561A pdb=" N HIS B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 447 removed outlier: 3.561A pdb=" N SER B 427 " --> pdb=" O ASN B 423 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 479 removed outlier: 5.156A pdb=" N THR B 476 " --> pdb=" O ALA B 472 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU B 477 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 485 removed outlier: 3.665A pdb=" N LEU B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 493 removed outlier: 3.694A pdb=" N GLY B 489 " --> pdb=" O GLY B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 505 Processing helix chain 'B' and resid 528 through 554 Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 564 through 587 removed outlier: 3.650A pdb=" N PHE B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 605 Processing helix chain 'B' and resid 621 through 646 removed outlier: 4.235A pdb=" N VAL B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 681 Processing helix chain 'B' and resid 684 through 706 removed outlier: 5.301A pdb=" N VAL B 697 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N TYR B 698 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE B 699 " --> pdb=" O VAL B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 720 removed outlier: 5.367A pdb=" N THR B 716 " --> pdb=" O PHE B 712 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N HIS B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 735 Processing helix chain 'B' and resid 764 through 819 removed outlier: 3.580A pdb=" N PHE B 818 " --> pdb=" O PHE B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 853 Processing helix chain 'B' and resid 854 through 858 removed outlier: 3.779A pdb=" N GLY B 857 " --> pdb=" O GLY B 854 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG B 858 " --> pdb=" O LEU B 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 854 through 858' Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56 removed outlier: 6.049A pdb=" N HIS B 175 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ARG B 200 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N THR B 332 " --> pdb=" O ARG B 200 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN B 346 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B 352 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 232 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N CYS B 287 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE B 234 " --> pdb=" O CYS B 287 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL B 289 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 236 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N MET B 233 " --> pdb=" O ALA B 379 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N MET B 381 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N CYS B 235 " --> pdb=" O MET B 381 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG B 461 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N GLY B 406 " --> pdb=" O ARG B 461 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N HIS B 514 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA B 408 " --> pdb=" O HIS B 514 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL B 516 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLY B 410 " --> pdb=" O VAL B 516 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ASP B 518 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N LEU B 412 " --> pdb=" O ASP B 518 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL B 520 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 9.251A pdb=" N VAL B 414 " --> pdb=" O VAL B 520 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG B 522 " --> pdb=" O VAL B 414 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 386 through 387 removed outlier: 7.645A pdb=" N HIS A 514 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA A 408 " --> pdb=" O HIS A 514 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL A 516 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY A 410 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ASP A 518 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N LEU A 412 " --> pdb=" O ASP A 518 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL A 520 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 9.251A pdb=" N VAL A 414 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG A 522 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N GLY A 406 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG A 461 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N MET A 233 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N MET A 381 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N CYS A 235 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU A 232 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N CYS A 287 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE A 234 " --> pdb=" O CYS A 287 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL A 289 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE A 236 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN A 346 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS A 352 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N THR A 332 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ARG A 200 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N HIS A 175 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL A 174 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER B 55 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LYS A 176 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AA4, first strand: chain 'B' and resid 336 through 337 855 hydrogen bonds defined for protein. 2517 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4088 1.34 - 1.46: 2260 1.46 - 1.57: 6932 1.57 - 1.69: 6 1.69 - 1.81: 118 Bond restraints: 13404 Sorted by residual: bond pdb=" O1' UD1 A1001 " pdb=" PB UD1 A1001 " ideal model delta sigma weight residual 1.658 1.563 0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" O1' UD1 B1001 " pdb=" PB UD1 B1001 " ideal model delta sigma weight residual 1.658 1.563 0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" O5B UD1 B1001 " pdb=" PA UD1 B1001 " ideal model delta sigma weight residual 1.645 1.582 0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" O5B UD1 A1001 " pdb=" PA UD1 A1001 " ideal model delta sigma weight residual 1.645 1.582 0.063 2.00e-02 2.50e+03 9.81e+00 bond pdb=" O3A UD1 B1001 " pdb=" PA UD1 B1001 " ideal model delta sigma weight residual 1.642 1.586 0.056 2.00e-02 2.50e+03 7.89e+00 ... (remaining 13399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 18154 3.84 - 7.69: 46 7.69 - 11.53: 2 11.53 - 15.38: 2 15.38 - 19.22: 2 Bond angle restraints: 18206 Sorted by residual: angle pdb=" O1' UD1 A1001 " pdb=" PB UD1 A1001 " pdb=" O3A UD1 A1001 " ideal model delta sigma weight residual 92.88 112.10 -19.22 3.00e+00 1.11e-01 4.10e+01 angle pdb=" O1' UD1 B1001 " pdb=" PB UD1 B1001 " pdb=" O3A UD1 B1001 " ideal model delta sigma weight residual 92.88 112.10 -19.22 3.00e+00 1.11e-01 4.10e+01 angle pdb=" PA UD1 B1001 " pdb=" O3A UD1 B1001 " pdb=" PB UD1 B1001 " ideal model delta sigma weight residual 122.84 137.31 -14.47 3.00e+00 1.11e-01 2.33e+01 angle pdb=" PA UD1 A1001 " pdb=" O3A UD1 A1001 " pdb=" PB UD1 A1001 " ideal model delta sigma weight residual 122.84 137.29 -14.45 3.00e+00 1.11e-01 2.32e+01 angle pdb=" C SER A 615 " pdb=" N GLU A 616 " pdb=" CA GLU A 616 " ideal model delta sigma weight residual 121.71 116.60 5.11 1.39e+00 5.18e-01 1.35e+01 ... (remaining 18201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.93: 7254 14.93 - 29.86: 431 29.86 - 44.80: 83 44.80 - 59.73: 14 59.73 - 74.66: 6 Dihedral angle restraints: 7788 sinusoidal: 3054 harmonic: 4734 Sorted by residual: dihedral pdb=" CA GLN A 602 " pdb=" C GLN A 602 " pdb=" N GLY A 603 " pdb=" CA GLY A 603 " ideal model delta harmonic sigma weight residual 180.00 161.36 18.64 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA GLN B 602 " pdb=" C GLN B 602 " pdb=" N GLY B 603 " pdb=" CA GLY B 603 " ideal model delta harmonic sigma weight residual 180.00 161.43 18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ASN A 607 " pdb=" CB ASN A 607 " pdb=" CG ASN A 607 " pdb=" OD1 ASN A 607 " ideal model delta sinusoidal sigma weight residual -90.00 -153.48 63.48 2 2.00e+01 2.50e-03 9.61e+00 ... (remaining 7785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1623 0.047 - 0.095: 314 0.095 - 0.142: 63 0.142 - 0.189: 0 0.189 - 0.237: 2 Chirality restraints: 2002 Sorted by residual: chirality pdb=" C1B UD1 A1001 " pdb=" C2B UD1 A1001 " pdb=" N1 UD1 A1001 " pdb=" O4B UD1 A1001 " both_signs ideal model delta sigma weight residual False 2.20 2.44 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C1B UD1 B1001 " pdb=" C2B UD1 B1001 " pdb=" N1 UD1 B1001 " pdb=" O4B UD1 B1001 " both_signs ideal model delta sigma weight residual False 2.20 2.44 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C1' UD1 A1001 " pdb=" C2' UD1 A1001 " pdb=" O1' UD1 A1001 " pdb=" O5' UD1 A1001 " both_signs ideal model delta sigma weight residual False -2.21 -2.34 0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1999 not shown) Planarity restraints: 2292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 437 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.23e+00 pdb=" C ASN A 437 " 0.043 2.00e-02 2.50e+03 pdb=" O ASN A 437 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE A 438 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 437 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C ASN B 437 " -0.043 2.00e-02 2.50e+03 pdb=" O ASN B 437 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE B 438 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 598 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.09e+00 pdb=" C PHE A 598 " 0.039 2.00e-02 2.50e+03 pdb=" O PHE A 598 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE A 599 " -0.013 2.00e-02 2.50e+03 ... (remaining 2289 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2328 2.77 - 3.30: 12056 3.30 - 3.83: 21093 3.83 - 4.37: 22778 4.37 - 4.90: 42685 Nonbonded interactions: 100940 Sorted by model distance: nonbonded pdb=" OH TYR A 52 " pdb=" OE2 GLU B 225 " model vdw 2.235 3.040 nonbonded pdb=" OD1 ASN A 109 " pdb=" NH2 ARG A 171 " model vdw 2.249 3.120 nonbonded pdb=" OD1 ASN B 109 " pdb=" NH2 ARG B 171 " model vdw 2.249 3.120 nonbonded pdb=" O GLU A 241 " pdb=" OG1 THR A 300 " model vdw 2.303 3.040 nonbonded pdb=" O GLU B 241 " pdb=" OG1 THR B 300 " model vdw 2.303 3.040 ... (remaining 100935 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.050 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.290 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 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 : 0.004 0.095 13404 Z= 0.170 Angle : 0.586 19.220 18206 Z= 0.286 Chirality : 0.039 0.237 2002 Planarity : 0.004 0.043 2292 Dihedral : 10.177 74.658 4748 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.58 % Allowed : 5.33 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.22), residues: 1604 helix: 2.65 (0.17), residues: 1006 sheet: -0.26 (0.41), residues: 166 loop : -1.19 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 608 TYR 0.008 0.001 TYR A 365 PHE 0.012 0.001 PHE A 601 TRP 0.010 0.001 TRP A 804 HIS 0.002 0.001 HIS B 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (13404) covalent geometry : angle 0.58561 / 0.29 (18206) hydrogen bonds : bond 0.10966 / 7.17 ( 855) hydrogen bonds : angle 4.98108 / 3.53 ( 2517) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 250 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ILE cc_start: 0.6431 (OUTLIER) cc_final: 0.6085 (mt) REVERT: A 327 HIS cc_start: 0.8676 (OUTLIER) cc_final: 0.8239 (m-70) REVERT: A 738 GLN cc_start: 0.8155 (pm20) cc_final: 0.7368 (pm20) REVERT: A 785 ARG cc_start: 0.7497 (ttm110) cc_final: 0.7020 (ttp80) REVERT: B 183 ASN cc_start: 0.7151 (m-40) cc_final: 0.6805 (p0) REVERT: B 403 HIS cc_start: 0.6930 (t-90) cc_final: 0.6641 (t-90) REVERT: B 552 TRP cc_start: 0.7593 (t-100) cc_final: 0.5244 (m-10) REVERT: B 790 LYS cc_start: 0.8149 (tttt) cc_final: 0.7920 (tttp) outliers start: 8 outliers final: 5 residues processed: 258 average time/residue: 0.1032 time to fit residues: 39.3425 Evaluate side-chains 157 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 150 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 617 TYR Chi-restraints excluded: chain B residue 651 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.0030 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.4968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 ASN A 478 ASN A 607 ASN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 GLN B 402 ASN B 607 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.151701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.118321 restraints weight = 15621.685| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.84 r_work: 0.3210 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13404 Z= 0.124 Angle : 0.493 7.683 18206 Z= 0.260 Chirality : 0.038 0.133 2002 Planarity : 0.004 0.044 2292 Dihedral : 5.348 59.978 1790 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.02 % Allowed : 9.29 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.22), residues: 1604 helix: 2.66 (0.17), residues: 1012 sheet: -0.36 (0.42), residues: 170 loop : -0.95 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 199 TYR 0.008 0.001 TYR A 732 PHE 0.014 0.001 PHE A 601 TRP 0.008 0.001 TRP A 804 HIS 0.002 0.001 HIS A 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (13404) covalent geometry : angle 0.49275 / 0.26 (18206) hydrogen bonds : bond 0.05133 / 3.50 ( 855) hydrogen bonds : angle 4.50843 / 3.23 ( 2517) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.6156 (OUTLIER) cc_final: 0.5745 (mt) REVERT: A 71 MET cc_start: 0.1102 (ttm) cc_final: 0.0498 (mtt) REVERT: A 730 THR cc_start: 0.8877 (m) cc_final: 0.8588 (p) REVERT: A 738 GLN cc_start: 0.8397 (pm20) cc_final: 0.7523 (pm20) REVERT: A 785 ARG cc_start: 0.7888 (ttm110) cc_final: 0.7344 (ttp80) REVERT: B 75 MET cc_start: 0.3216 (mpp) cc_final: 0.2880 (tpt) REVERT: B 183 ASN cc_start: 0.7322 (m-40) cc_final: 0.6988 (p0) REVERT: B 229 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7526 (mtm-85) REVERT: B 463 GLU cc_start: 0.7950 (tt0) cc_final: 0.7746 (mt-10) REVERT: B 552 TRP cc_start: 0.7772 (t-100) cc_final: 0.4992 (m-10) REVERT: B 666 MET cc_start: 0.8445 (ttp) cc_final: 0.8226 (ttm) REVERT: B 780 ARG cc_start: 0.7471 (mtm110) cc_final: 0.6982 (ptp-110) REVERT: B 790 LYS cc_start: 0.8272 (tttt) cc_final: 0.8041 (tttp) outliers start: 28 outliers final: 11 residues processed: 189 average time/residue: 0.0937 time to fit residues: 26.5582 Evaluate side-chains 158 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 651 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 34 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 37 optimal weight: 0.0070 chunk 17 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 overall best weight: 0.8602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 263 GLN B 263 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.148396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114937 restraints weight = 15824.831| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.93 r_work: 0.3171 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13404 Z= 0.142 Angle : 0.500 11.284 18206 Z= 0.263 Chirality : 0.038 0.134 2002 Planarity : 0.004 0.049 2292 Dihedral : 5.258 59.368 1786 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.24 % Favored : 94.70 % Rotamer: Outliers : 2.09 % Allowed : 10.45 % Favored : 87.46 % 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 are not related in a simple way. whole: 2.05 (0.22), residues: 1604 helix: 2.62 (0.17), residues: 1000 sheet: -0.51 (0.41), residues: 174 loop : -0.93 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 199 TYR 0.012 0.001 TYR A 219 PHE 0.025 0.001 PHE B 397 TRP 0.007 0.001 TRP A 804 HIS 0.003 0.001 HIS A 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (13404) covalent geometry : angle 0.50029 / 0.26 (18206) hydrogen bonds : bond 0.05535 / 3.79 ( 855) hydrogen bonds : angle 4.49389 / 3.23 ( 2517) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.318 Fit side-chains REVERT: A 37 ILE cc_start: 0.6227 (OUTLIER) cc_final: 0.5800 (mt) REVERT: A 71 MET cc_start: 0.0917 (ttm) cc_final: 0.0402 (mtt) REVERT: A 161 ILE cc_start: 0.8336 (tp) cc_final: 0.8015 (tt) REVERT: A 206 VAL cc_start: 0.8723 (m) cc_final: 0.8472 (t) REVERT: A 229 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7601 (mtm-85) REVERT: A 713 MET cc_start: 0.8516 (mmt) cc_final: 0.8001 (mpp) REVERT: B 75 MET cc_start: 0.3598 (mpp) cc_final: 0.3341 (tpt) REVERT: B 183 ASN cc_start: 0.7373 (m-40) cc_final: 0.7049 (p0) REVERT: B 229 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7578 (mtm-85) REVERT: B 371 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8220 (mm-30) REVERT: B 552 TRP cc_start: 0.7771 (t-100) cc_final: 0.4791 (m-10) REVERT: B 790 LYS cc_start: 0.8253 (tttt) cc_final: 0.8039 (tttp) outliers start: 29 outliers final: 18 residues processed: 172 average time/residue: 0.0891 time to fit residues: 23.0949 Evaluate side-chains 159 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 39 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 chunk 24 optimal weight: 0.0470 chunk 50 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 134 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.149506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.115970 restraints weight = 15671.879| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.78 r_work: 0.3167 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13404 Z= 0.120 Angle : 0.475 9.321 18206 Z= 0.250 Chirality : 0.037 0.131 2002 Planarity : 0.004 0.048 2292 Dihedral : 5.144 57.982 1784 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.99 % Favored : 94.89 % Rotamer: Outliers : 2.02 % Allowed : 11.60 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.22), residues: 1604 helix: 2.64 (0.17), residues: 1000 sheet: -0.50 (0.41), residues: 174 loop : -0.90 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 199 TYR 0.008 0.001 TYR A 219 PHE 0.018 0.001 PHE B 397 TRP 0.005 0.001 TRP B 804 HIS 0.002 0.001 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (13404) covalent geometry : angle 0.47497 / 0.25 (18206) hydrogen bonds : bond 0.05126 / 3.51 ( 855) hydrogen bonds : angle 4.44890 / 3.20 ( 2517) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.412 Fit side-chains REVERT: A 37 ILE cc_start: 0.6164 (OUTLIER) cc_final: 0.5767 (mt) REVERT: A 71 MET cc_start: 0.0877 (ttm) cc_final: 0.0393 (mtt) REVERT: A 161 ILE cc_start: 0.8296 (tp) cc_final: 0.7969 (tt) REVERT: A 229 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7586 (mtm-85) REVERT: A 651 HIS cc_start: 0.7033 (OUTLIER) cc_final: 0.5440 (p-80) REVERT: A 713 MET cc_start: 0.8510 (mmt) cc_final: 0.7987 (mpp) REVERT: B 75 MET cc_start: 0.3805 (mpp) cc_final: 0.3307 (tpt) REVERT: B 183 ASN cc_start: 0.7332 (m-40) cc_final: 0.7053 (p0) REVERT: B 371 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8221 (mm-30) REVERT: B 552 TRP cc_start: 0.7757 (t-100) cc_final: 0.4784 (m-10) REVERT: B 651 HIS cc_start: 0.6806 (OUTLIER) cc_final: 0.5521 (p-80) REVERT: B 780 ARG cc_start: 0.7331 (mtm110) cc_final: 0.6825 (ptp-110) REVERT: B 790 LYS cc_start: 0.8201 (tttt) cc_final: 0.7994 (tttp) outliers start: 28 outliers final: 13 residues processed: 175 average time/residue: 0.1089 time to fit residues: 28.7535 Evaluate side-chains 158 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 617 TYR Chi-restraints excluded: chain B residue 651 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 45 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.147340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.113857 restraints weight = 15985.760| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.97 r_work: 0.3083 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13404 Z= 0.169 Angle : 0.523 9.671 18206 Z= 0.274 Chirality : 0.039 0.132 2002 Planarity : 0.004 0.050 2292 Dihedral : 5.193 57.709 1784 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.36 % Favored : 94.51 % Rotamer: Outliers : 2.74 % Allowed : 12.03 % Favored : 85.23 % 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 are not related in a simple way. whole: 1.89 (0.22), residues: 1604 helix: 2.48 (0.17), residues: 1000 sheet: -0.50 (0.41), residues: 174 loop : -0.98 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 164 TYR 0.011 0.001 TYR A 219 PHE 0.014 0.001 PHE B 601 TRP 0.007 0.001 TRP B 804 HIS 0.003 0.001 HIS A 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (13404) covalent geometry : angle 0.52267 / 0.27 (18206) hydrogen bonds : bond 0.05923 / 4.06 ( 855) hydrogen bonds : angle 4.54156 / 3.26 ( 2517) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.323 Fit side-chains REVERT: A 37 ILE cc_start: 0.6309 (OUTLIER) cc_final: 0.5844 (mt) REVERT: A 161 ILE cc_start: 0.8443 (tp) cc_final: 0.8173 (tt) REVERT: A 229 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7627 (mtm-85) REVERT: A 651 HIS cc_start: 0.7144 (OUTLIER) cc_final: 0.5514 (p-80) REVERT: B 75 MET cc_start: 0.3573 (mpp) cc_final: 0.3264 (tpt) REVERT: B 183 ASN cc_start: 0.7470 (m-40) cc_final: 0.7167 (p0) REVERT: B 229 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7572 (mtm-85) REVERT: B 371 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8530 (mm-30) REVERT: B 651 HIS cc_start: 0.6745 (OUTLIER) cc_final: 0.5413 (p-80) outliers start: 38 outliers final: 27 residues processed: 178 average time/residue: 0.1058 time to fit residues: 28.0256 Evaluate side-chains 173 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 403 HIS Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 617 TYR Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 159 optimal weight: 0.7980 chunk 128 optimal weight: 0.2980 chunk 105 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 139 optimal weight: 0.5980 chunk 121 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.149929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116780 restraints weight = 15812.572| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.03 r_work: 0.3147 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13404 Z= 0.124 Angle : 0.490 10.823 18206 Z= 0.256 Chirality : 0.038 0.137 2002 Planarity : 0.004 0.047 2292 Dihedral : 5.125 58.773 1784 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.31 % Allowed : 13.11 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.22), residues: 1604 helix: 2.59 (0.17), residues: 1000 sheet: -0.47 (0.41), residues: 174 loop : -0.97 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 780 TYR 0.010 0.001 TYR B 492 PHE 0.013 0.001 PHE B 601 TRP 0.006 0.001 TRP B 804 HIS 0.002 0.001 HIS B 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (13404) covalent geometry : angle 0.48951 / 0.26 (18206) hydrogen bonds : bond 0.05168 / 3.55 ( 855) hydrogen bonds : angle 4.46872 / 3.22 ( 2517) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.332 Fit side-chains REVERT: A 37 ILE cc_start: 0.6370 (OUTLIER) cc_final: 0.5954 (mt) REVERT: A 161 ILE cc_start: 0.8380 (tp) cc_final: 0.8089 (tt) REVERT: A 229 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7541 (mtm-85) REVERT: A 238 MET cc_start: 0.8929 (ttp) cc_final: 0.8648 (ptm) REVERT: A 651 HIS cc_start: 0.7124 (OUTLIER) cc_final: 0.5467 (p-80) REVERT: B 75 MET cc_start: 0.3711 (mpp) cc_final: 0.3148 (tpt) REVERT: B 183 ASN cc_start: 0.7436 (m-40) cc_final: 0.7132 (p0) REVERT: B 229 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7501 (mtm-85) REVERT: B 263 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8851 (tt0) REVERT: B 371 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8448 (mm-30) REVERT: B 552 TRP cc_start: 0.7841 (t-100) cc_final: 0.4741 (m-10) REVERT: B 651 HIS cc_start: 0.6777 (OUTLIER) cc_final: 0.5389 (p-80) outliers start: 32 outliers final: 23 residues processed: 170 average time/residue: 0.0942 time to fit residues: 24.4890 Evaluate side-chains 166 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 617 TYR Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 76 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 152 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.147189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.113913 restraints weight = 15853.692| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.96 r_work: 0.3114 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13404 Z= 0.143 Angle : 0.502 10.289 18206 Z= 0.264 Chirality : 0.038 0.133 2002 Planarity : 0.004 0.048 2292 Dihedral : 5.129 58.442 1784 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.81 % Allowed : 12.61 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.22), residues: 1604 helix: 2.53 (0.17), residues: 1002 sheet: -0.49 (0.41), residues: 174 loop : -0.98 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 199 TYR 0.010 0.001 TYR B 239 PHE 0.014 0.001 PHE B 545 TRP 0.006 0.001 TRP B 804 HIS 0.003 0.001 HIS B 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (13404) covalent geometry : angle 0.50198 / 0.26 (18206) hydrogen bonds : bond 0.05400 / 3.70 ( 855) hydrogen bonds : angle 4.48013 / 3.23 ( 2517) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 0.735 Fit side-chains REVERT: A 37 ILE cc_start: 0.6297 (OUTLIER) cc_final: 0.5892 (mt) REVERT: A 161 ILE cc_start: 0.8384 (tp) cc_final: 0.8093 (tt) REVERT: A 229 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7573 (mtm-85) REVERT: A 651 HIS cc_start: 0.7140 (OUTLIER) cc_final: 0.5659 (p-80) REVERT: B 75 MET cc_start: 0.3730 (mpp) cc_final: 0.3147 (tpt) REVERT: B 183 ASN cc_start: 0.7515 (m-40) cc_final: 0.7216 (p0) REVERT: B 229 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7519 (mtm-85) REVERT: B 552 TRP cc_start: 0.7795 (t-100) cc_final: 0.4714 (m-10) REVERT: B 651 HIS cc_start: 0.6926 (OUTLIER) cc_final: 0.5522 (p-80) REVERT: B 667 MET cc_start: 0.8018 (tpp) cc_final: 0.7692 (tpt) outliers start: 39 outliers final: 29 residues processed: 169 average time/residue: 0.1044 time to fit residues: 27.0250 Evaluate side-chains 167 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 617 TYR Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 851 HIS Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 88 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.148738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.115670 restraints weight = 15764.699| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.93 r_work: 0.3121 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13404 Z= 0.139 Angle : 0.506 9.121 18206 Z= 0.265 Chirality : 0.038 0.131 2002 Planarity : 0.004 0.048 2292 Dihedral : 5.121 58.277 1784 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.88 % Allowed : 12.54 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.22), residues: 1604 helix: 2.52 (0.17), residues: 1002 sheet: -0.46 (0.41), residues: 174 loop : -0.99 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 199 TYR 0.009 0.001 TYR B 239 PHE 0.014 0.001 PHE A 601 TRP 0.006 0.001 TRP B 804 HIS 0.002 0.001 HIS B 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (13404) covalent geometry : angle 0.50617 / 0.27 (18206) hydrogen bonds : bond 0.05374 / 3.68 ( 855) hydrogen bonds : angle 4.47774 / 3.22 ( 2517) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.497 Fit side-chains REVERT: A 37 ILE cc_start: 0.6431 (OUTLIER) cc_final: 0.6032 (mt) REVERT: A 161 ILE cc_start: 0.8389 (tp) cc_final: 0.8088 (tt) REVERT: A 229 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7587 (mtm-85) REVERT: A 651 HIS cc_start: 0.7087 (OUTLIER) cc_final: 0.5898 (p-80) REVERT: B 75 MET cc_start: 0.3452 (mpp) cc_final: 0.2950 (tpt) REVERT: B 183 ASN cc_start: 0.7527 (m-40) cc_final: 0.7235 (p0) REVERT: B 229 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7541 (mtm-85) REVERT: B 651 HIS cc_start: 0.6905 (OUTLIER) cc_final: 0.5417 (p-80) REVERT: B 787 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7662 (tm-30) outliers start: 40 outliers final: 31 residues processed: 172 average time/residue: 0.1016 time to fit residues: 26.5391 Evaluate side-chains 167 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 617 TYR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 617 TYR Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 851 HIS Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 87 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 133 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.147412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.114239 restraints weight = 16012.500| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.97 r_work: 0.3093 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13404 Z= 0.159 Angle : 0.531 11.213 18206 Z= 0.278 Chirality : 0.039 0.131 2002 Planarity : 0.004 0.049 2292 Dihedral : 5.160 57.337 1784 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.81 % Allowed : 13.11 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.22), residues: 1604 helix: 2.45 (0.17), residues: 1004 sheet: -0.49 (0.41), residues: 174 loop : -0.99 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 199 TYR 0.010 0.001 TYR B 239 PHE 0.015 0.001 PHE A 545 TRP 0.007 0.001 TRP B 804 HIS 0.003 0.001 HIS B 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (13404) covalent geometry : angle 0.53142 / 0.28 (18206) hydrogen bonds : bond 0.05696 / 3.92 ( 855) hydrogen bonds : angle 4.53588 / 3.27 ( 2517) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 0.424 Fit side-chains REVERT: A 37 ILE cc_start: 0.6377 (OUTLIER) cc_final: 0.5946 (mt) REVERT: A 229 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7605 (mtm-85) REVERT: A 651 HIS cc_start: 0.7226 (OUTLIER) cc_final: 0.6223 (p-80) REVERT: B 75 MET cc_start: 0.3482 (mpp) cc_final: 0.3054 (tpt) REVERT: B 183 ASN cc_start: 0.7549 (m-40) cc_final: 0.7256 (p0) REVERT: B 229 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7527 (mtm-85) REVERT: B 651 HIS cc_start: 0.6975 (OUTLIER) cc_final: 0.5450 (p-80) REVERT: B 667 MET cc_start: 0.8025 (tpp) cc_final: 0.7751 (tpt) outliers start: 39 outliers final: 32 residues processed: 164 average time/residue: 0.1051 time to fit residues: 26.0836 Evaluate side-chains 166 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 617 TYR Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 851 HIS Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 113 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.148713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.115485 restraints weight = 15933.922| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.92 r_work: 0.3111 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13404 Z= 0.137 Angle : 0.517 9.703 18206 Z= 0.271 Chirality : 0.038 0.131 2002 Planarity : 0.004 0.048 2292 Dihedral : 5.156 58.143 1784 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.59 % Allowed : 13.54 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.22), residues: 1604 helix: 2.52 (0.17), residues: 1000 sheet: -0.47 (0.41), residues: 174 loop : -1.03 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 199 TYR 0.011 0.001 TYR B 492 PHE 0.015 0.001 PHE B 545 TRP 0.006 0.001 TRP B 804 HIS 0.002 0.001 HIS B 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (13404) covalent geometry : angle 0.51699 / 0.27 (18206) hydrogen bonds : bond 0.05329 / 3.66 ( 855) hydrogen bonds : angle 4.50615 / 3.25 ( 2517) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.511 Fit side-chains REVERT: A 37 ILE cc_start: 0.6429 (OUTLIER) cc_final: 0.6020 (mt) REVERT: A 229 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7507 (mtm-85) REVERT: A 238 MET cc_start: 0.9005 (ttp) cc_final: 0.8689 (ptm) REVERT: A 651 HIS cc_start: 0.7136 (OUTLIER) cc_final: 0.6150 (p-80) REVERT: B 75 MET cc_start: 0.3744 (mpp) cc_final: 0.3124 (tpt) REVERT: B 183 ASN cc_start: 0.7531 (m-40) cc_final: 0.7220 (p0) REVERT: B 229 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7550 (mtm-85) REVERT: B 651 HIS cc_start: 0.6963 (OUTLIER) cc_final: 0.5427 (p-80) REVERT: B 667 MET cc_start: 0.7953 (tpp) cc_final: 0.7643 (tpt) REVERT: B 787 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7658 (tm-30) outliers start: 36 outliers final: 30 residues processed: 165 average time/residue: 0.0909 time to fit residues: 23.0222 Evaluate side-chains 166 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 617 TYR Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 851 HIS Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 24 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 146 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.148689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115402 restraints weight = 15804.356| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.97 r_work: 0.3132 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13404 Z= 0.140 Angle : 0.526 9.929 18206 Z= 0.275 Chirality : 0.038 0.134 2002 Planarity : 0.004 0.048 2292 Dihedral : 5.146 58.125 1784 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.74 % Allowed : 13.76 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.22), residues: 1604 helix: 2.52 (0.17), residues: 1000 sheet: -0.48 (0.41), residues: 174 loop : -1.05 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 199 TYR 0.011 0.001 TYR A 492 PHE 0.048 0.001 PHE A 487 TRP 0.006 0.001 TRP B 804 HIS 0.002 0.001 HIS B 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (13404) covalent geometry : angle 0.52558 / 0.28 (18206) hydrogen bonds : bond 0.05362 / 3.70 ( 855) hydrogen bonds : angle 4.50423 / 3.24 ( 2517) =============================================================================== Job complete usr+sys time: 3216.99 seconds wall clock time: 55 minutes 49.57 seconds (3349.57 seconds total)