Starting phenix.real_space_refine on Wed Mar 4 10:15:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wjn_32546/03_2026/7wjn_32546.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wjn_32546/03_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_32546/03_2026/7wjn_32546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wjn_32546/03_2026/7wjn_32546.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wjn_32546/03_2026/7wjn_32546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wjn_32546/03_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-5986/lib/python3.9/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: 5.18, per 1000 atoms: 0.40 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: 1.06 Conformation dependent library (CDL) restraints added in 581.7 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: 0.43 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: 1.67 Time building geometry restraints manager: 1.46 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: 7316 14.93 - 29.86: 467 29.86 - 44.80: 89 44.80 - 59.73: 18 59.73 - 74.66: 6 Dihedral angle restraints: 7896 sinusoidal: 3162 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 7893 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: 0.01 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: 1.880 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.190 Find NCS groups from input model: 0.080 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 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 : 10.438 74.658 4856 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 covalent geometry : bond 0.00354 (13404) covalent geometry : angle 0.58561 (18206) hydrogen bonds : bond 0.10966 ( 855) hydrogen bonds : angle 4.98108 ( 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 : 0.490 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: 0.1081 time to fit residues: 40.4359 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 : 0.409 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 607 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.151681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118241 restraints weight = 15621.755| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.90 r_work: 0.3210 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1269 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= 0.122 Angle : 0.495 8.203 18206 Z= 0.261 Chirality : 0.038 0.134 2002 Planarity : 0.004 0.044 2292 Dihedral : 6.781 59.948 1898 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.95 % Allowed : 9.37 % 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: 2.16 (0.22), residues: 1604 helix: 2.66 (0.17), residues: 1012 sheet: -0.36 (0.42), residues: 170 loop : -0.94 (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 175 Details of bonding type rmsd covalent geometry : bond 0.00248 (13404) covalent geometry : angle 0.49477 (18206) hydrogen bonds : bond 0.05141 ( 855) hydrogen bonds : angle 4.50995 ( 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 191 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.6132 (OUTLIER) cc_final: 0.5721 (mt) REVERT: A 71 MET cc_start: 0.1090 (ttm) cc_final: 0.0486 (mtt) REVERT: A 730 THR cc_start: 0.8878 (m) cc_final: 0.8582 (p) REVERT: A 738 GLN cc_start: 0.8396 (pm20) cc_final: 0.7517 (pm20) REVERT: A 785 ARG cc_start: 0.7887 (ttm110) cc_final: 0.7328 (ttp80) REVERT: B 75 MET cc_start: 0.3345 (mpp) cc_final: 0.2870 (tpt) REVERT: B 183 ASN cc_start: 0.7307 (m-40) cc_final: 0.6963 (p0) REVERT: B 229 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7528 (mtm-85) REVERT: B 463 GLU cc_start: 0.7970 (tt0) cc_final: 0.7753 (mt-10) REVERT: B 552 TRP cc_start: 0.7759 (t-100) cc_final: 0.4973 (m-10) REVERT: B 666 MET cc_start: 0.8432 (ttp) cc_final: 0.8213 (ttm) REVERT: B 780 ARG cc_start: 0.7448 (mtm110) cc_final: 0.6952 (ptp-110) REVERT: B 790 LYS cc_start: 0.8260 (tttt) cc_final: 0.8028 (tttp) outliers start: 27 outliers final: 9 residues processed: 187 average time/residue: 0.1077 time to fit residues: 29.7086 Evaluate side-chains 156 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 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 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: 3.9990 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: 0.0570 chunk 17 optimal weight: 0.4980 chunk 109 optimal weight: 0.8980 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3741 r_free = 0.3741 target = 0.150491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.117285 restraints weight = 15777.448| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.86 r_work: 0.3204 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1571 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= 0.123 Angle : 0.481 11.197 18206 Z= 0.252 Chirality : 0.038 0.132 2002 Planarity : 0.004 0.048 2292 Dihedral : 6.576 63.178 1894 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.99 % Favored : 94.95 % Rotamer: Outliers : 1.66 % Allowed : 10.66 % Favored : 87.68 % 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: 2.70 (0.17), residues: 1000 sheet: -0.48 (0.41), residues: 174 loop : -0.89 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 199 TYR 0.009 0.001 TYR A 219 PHE 0.024 0.001 PHE B 397 TRP 0.007 0.001 TRP A 804 HIS 0.004 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00260 (13404) covalent geometry : angle 0.48109 (18206) hydrogen bonds : bond 0.05111 ( 855) hydrogen bonds : angle 4.43922 ( 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 177 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.470 Fit side-chains REVERT: A 37 ILE cc_start: 0.6132 (OUTLIER) cc_final: 0.5728 (mt) REVERT: A 71 MET cc_start: 0.0889 (ttm) cc_final: 0.0388 (mtt) REVERT: A 161 ILE cc_start: 0.8276 (tp) cc_final: 0.7933 (tt) REVERT: A 229 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7636 (mtm-85) REVERT: A 713 MET cc_start: 0.8538 (mmt) cc_final: 0.8030 (mpp) REVERT: B 75 MET cc_start: 0.3563 (mpp) cc_final: 0.3192 (tpt) REVERT: B 183 ASN cc_start: 0.7351 (m-40) cc_final: 0.7030 (p0) REVERT: B 371 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8161 (mm-30) REVERT: B 552 TRP cc_start: 0.7759 (t-100) cc_final: 0.4851 (m-10) REVERT: B 651 HIS cc_start: 0.6716 (OUTLIER) cc_final: 0.5419 (p-80) REVERT: B 790 LYS cc_start: 0.8257 (tttt) cc_final: 0.8032 (tttp) outliers start: 23 outliers final: 12 residues processed: 169 average time/residue: 0.1046 time to fit residues: 26.7528 Evaluate side-chains 156 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 204 THR 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: 0.6980 chunk 86 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3720 r_free = 0.3720 target = 0.148690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.115108 restraints weight = 15727.079| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.85 r_work: 0.3158 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1765 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= 0.136 Angle : 0.488 9.372 18206 Z= 0.256 Chirality : 0.038 0.133 2002 Planarity : 0.004 0.048 2292 Dihedral : 6.444 63.809 1892 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.36 % Favored : 94.51 % Rotamer: Outliers : 2.38 % Allowed : 11.17 % Favored : 86.46 % 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: 2.07 (0.22), residues: 1604 helix: 2.63 (0.17), residues: 1000 sheet: -0.47 (0.41), residues: 174 loop : -0.92 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 199 TYR 0.008 0.001 TYR B 239 PHE 0.019 0.001 PHE B 397 TRP 0.006 0.001 TRP B 804 HIS 0.003 0.001 HIS B 578 Details of bonding type rmsd covalent geometry : bond 0.00304 (13404) covalent geometry : angle 0.48797 (18206) hydrogen bonds : bond 0.05321 ( 855) hydrogen bonds : angle 4.46190 ( 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 181 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.489 Fit side-chains REVERT: A 37 ILE cc_start: 0.6222 (OUTLIER) cc_final: 0.5822 (mt) REVERT: A 71 MET cc_start: 0.0920 (ttm) cc_final: 0.0432 (mtt) REVERT: A 161 ILE cc_start: 0.8358 (tp) cc_final: 0.8025 (tt) REVERT: A 229 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7595 (mtm-85) REVERT: A 651 HIS cc_start: 0.7043 (OUTLIER) cc_final: 0.5436 (p-80) REVERT: A 713 MET cc_start: 0.8494 (mmt) cc_final: 0.7993 (mpp) REVERT: B 75 MET cc_start: 0.3667 (mpp) cc_final: 0.3295 (tpt) REVERT: B 183 ASN cc_start: 0.7359 (m-40) cc_final: 0.7103 (p0) REVERT: B 229 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7559 (mtm-85) REVERT: B 371 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8268 (mm-30) REVERT: B 552 TRP cc_start: 0.7779 (t-100) cc_final: 0.4803 (m-10) REVERT: B 651 HIS cc_start: 0.6675 (OUTLIER) cc_final: 0.5389 (p-80) REVERT: B 780 ARG cc_start: 0.7414 (mtm110) cc_final: 0.6915 (ptp-110) outliers start: 33 outliers final: 17 residues processed: 174 average time/residue: 0.1041 time to fit residues: 27.0578 Evaluate side-chains 164 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 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 564 THR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 204 THR 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 435 ILE Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 45 optimal weight: 0.4980 chunk 81 optimal weight: 0.0370 chunk 2 optimal weight: 0.3980 chunk 145 optimal weight: 0.0030 chunk 132 optimal weight: 1.9990 chunk 118 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 0.0870 chunk 107 optimal weight: 0.9980 overall best weight: 0.1846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.153917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.121051 restraints weight = 15728.588| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.97 r_work: 0.3247 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13404 Z= 0.103 Angle : 0.458 10.536 18206 Z= 0.238 Chirality : 0.036 0.127 2002 Planarity : 0.004 0.047 2292 Dihedral : 6.167 63.089 1892 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.37 % Allowed : 12.90 % Favored : 85.73 % 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: 2.28 (0.23), residues: 1604 helix: 2.83 (0.17), residues: 988 sheet: -0.44 (0.42), residues: 174 loop : -0.79 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 199 TYR 0.008 0.001 TYR B 492 PHE 0.018 0.001 PHE B 397 TRP 0.005 0.001 TRP B 202 HIS 0.002 0.000 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00193 (13404) covalent geometry : angle 0.45818 (18206) hydrogen bonds : bond 0.04276 ( 855) hydrogen bonds : angle 4.34658 ( 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 181 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.470 Fit side-chains REVERT: A 37 ILE cc_start: 0.6207 (OUTLIER) cc_final: 0.5837 (mt) REVERT: A 71 MET cc_start: 0.1889 (ttm) cc_final: 0.0808 (mtt) REVERT: A 102 ASP cc_start: 0.7985 (t0) cc_final: 0.7764 (t0) REVERT: A 229 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7538 (mtm-85) REVERT: A 238 MET cc_start: 0.8939 (ttp) cc_final: 0.8647 (ptm) REVERT: A 371 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8147 (mm-30) REVERT: A 552 TRP cc_start: 0.7762 (t-100) cc_final: 0.4518 (m-10) REVERT: A 651 HIS cc_start: 0.6910 (OUTLIER) cc_final: 0.5247 (p-80) REVERT: A 713 MET cc_start: 0.8560 (mmt) cc_final: 0.8053 (mpp) REVERT: B 75 MET cc_start: 0.3681 (mpp) cc_final: 0.3159 (tpt) REVERT: B 183 ASN cc_start: 0.7324 (m-40) cc_final: 0.7066 (p0) REVERT: B 229 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7499 (mtm-85) REVERT: B 371 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8201 (mm-30) REVERT: B 552 TRP cc_start: 0.7820 (t-100) cc_final: 0.4880 (m-10) REVERT: B 651 HIS cc_start: 0.6813 (OUTLIER) cc_final: 0.5502 (p-80) outliers start: 19 outliers final: 8 residues processed: 177 average time/residue: 0.0933 time to fit residues: 25.5580 Evaluate side-chains 155 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 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 229 ARG Chi-restraints excluded: chain A residue 327 HIS 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 851 HIS Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 651 HIS 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: 2.9990 chunk 105 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 139 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 78 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.152027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.119021 restraints weight = 15810.878| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.95 r_work: 0.3171 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13404 Z= 0.125 Angle : 0.476 8.611 18206 Z= 0.249 Chirality : 0.038 0.128 2002 Planarity : 0.004 0.046 2292 Dihedral : 6.144 61.899 1892 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.09 % Allowed : 13.11 % Favored : 84.80 % 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: 2.17 (0.23), residues: 1604 helix: 2.76 (0.17), residues: 994 sheet: -0.50 (0.41), residues: 174 loop : -0.93 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 199 TYR 0.010 0.001 TYR A 492 PHE 0.026 0.001 PHE A 397 TRP 0.006 0.001 TRP A 804 HIS 0.002 0.001 HIS B 578 Details of bonding type rmsd covalent geometry : bond 0.00270 (13404) covalent geometry : angle 0.47648 (18206) hydrogen bonds : bond 0.04902 ( 855) hydrogen bonds : angle 4.37060 ( 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: 29 poor density : 147 time to evaluate : 0.326 Fit side-chains REVERT: A 37 ILE cc_start: 0.6236 (OUTLIER) cc_final: 0.5856 (mt) REVERT: A 71 MET cc_start: 0.1589 (ttm) cc_final: 0.0562 (mtt) REVERT: A 102 ASP cc_start: 0.8069 (t0) cc_final: 0.7839 (t0) REVERT: A 161 ILE cc_start: 0.8434 (tp) cc_final: 0.8089 (tt) REVERT: A 229 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7582 (mtm-85) REVERT: A 238 MET cc_start: 0.8988 (ttp) cc_final: 0.8675 (ptm) REVERT: A 371 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8271 (mm-30) REVERT: A 651 HIS cc_start: 0.7063 (OUTLIER) cc_final: 0.5628 (p-80) REVERT: A 713 MET cc_start: 0.8559 (mmt) cc_final: 0.8038 (mpp) REVERT: B 75 MET cc_start: 0.3758 (mpp) cc_final: 0.3148 (tpt) REVERT: B 183 ASN cc_start: 0.7389 (m-40) cc_final: 0.7124 (p0) REVERT: B 229 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7525 (mtm-85) REVERT: B 371 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8328 (mm-30) REVERT: B 552 TRP cc_start: 0.7917 (t-100) cc_final: 0.4864 (m-10) REVERT: B 651 HIS cc_start: 0.6912 (OUTLIER) cc_final: 0.5656 (p-80) outliers start: 29 outliers final: 18 residues processed: 167 average time/residue: 0.0969 time to fit residues: 24.7951 Evaluate side-chains 165 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 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 688 ILE Chi-restraints excluded: chain A residue 852 THR 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 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 851 HIS 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: 2.9990 chunk 122 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 152 optimal weight: 0.4980 chunk 128 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.148043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.114888 restraints weight = 15815.434| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.95 r_work: 0.3134 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13404 Z= 0.137 Angle : 0.500 11.023 18206 Z= 0.261 Chirality : 0.038 0.129 2002 Planarity : 0.004 0.047 2292 Dihedral : 6.188 61.014 1892 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.38 % Allowed : 13.47 % Favored : 84.15 % 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: 2.07 (0.22), residues: 1604 helix: 2.64 (0.17), residues: 1000 sheet: -0.48 (0.41), residues: 174 loop : -0.95 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 199 TYR 0.010 0.001 TYR A 492 PHE 0.023 0.001 PHE A 397 TRP 0.005 0.001 TRP A 804 HIS 0.003 0.001 HIS B 578 Details of bonding type rmsd covalent geometry : bond 0.00305 (13404) covalent geometry : angle 0.49994 (18206) hydrogen bonds : bond 0.05266 ( 855) hydrogen bonds : angle 4.42771 ( 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: 33 poor density : 143 time to evaluate : 0.417 Fit side-chains REVERT: A 37 ILE cc_start: 0.6322 (OUTLIER) cc_final: 0.5910 (mt) REVERT: A 71 MET cc_start: 0.1626 (ttm) cc_final: 0.0618 (mtt) REVERT: A 102 ASP cc_start: 0.8141 (t0) cc_final: 0.7919 (t0) REVERT: A 161 ILE cc_start: 0.8418 (tp) cc_final: 0.8082 (tt) REVERT: A 229 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7563 (mtm-85) REVERT: A 299 LYS cc_start: 0.8380 (mmtt) cc_final: 0.8081 (mmtt) REVERT: A 371 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8273 (mm-30) REVERT: A 651 HIS cc_start: 0.7062 (OUTLIER) cc_final: 0.6006 (p-80) REVERT: A 713 MET cc_start: 0.8453 (mmt) cc_final: 0.7906 (mpp) REVERT: B 75 MET cc_start: 0.3750 (mpp) cc_final: 0.3111 (tpt) REVERT: B 183 ASN cc_start: 0.7510 (m-40) cc_final: 0.7239 (p0) REVERT: B 229 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7527 (mtm-85) REVERT: B 552 TRP cc_start: 0.7862 (t-100) cc_final: 0.4735 (m-10) REVERT: B 651 HIS cc_start: 0.7112 (OUTLIER) cc_final: 0.6242 (p-80) REVERT: B 667 MET cc_start: 0.8054 (tpp) cc_final: 0.7706 (tpt) outliers start: 33 outliers final: 23 residues processed: 165 average time/residue: 0.0988 time to fit residues: 24.8540 Evaluate side-chains 162 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 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 493 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 671 SER Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain A residue 852 THR 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 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 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: 0.9990 chunk 52 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 156 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 93 optimal weight: 0.0370 chunk 25 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 13 optimal weight: 0.0010 overall best weight: 0.4664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 647 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.150323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.117899 restraints weight = 15563.533| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.90 r_work: 0.3179 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13404 Z= 0.111 Angle : 0.479 8.919 18206 Z= 0.249 Chirality : 0.037 0.134 2002 Planarity : 0.004 0.046 2292 Dihedral : 6.061 60.294 1892 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.95 % Allowed : 14.27 % Favored : 83.79 % 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: 2.16 (0.22), residues: 1604 helix: 2.70 (0.17), residues: 1002 sheet: -0.46 (0.41), residues: 174 loop : -0.87 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 199 TYR 0.007 0.001 TYR B 239 PHE 0.022 0.001 PHE A 397 TRP 0.005 0.001 TRP A 804 HIS 0.002 0.000 HIS B 578 Details of bonding type rmsd covalent geometry : bond 0.00230 (13404) covalent geometry : angle 0.47898 (18206) hydrogen bonds : bond 0.04682 ( 855) hydrogen bonds : angle 4.36523 ( 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 167 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.474 Fit side-chains REVERT: A 71 MET cc_start: 0.1686 (ttm) cc_final: 0.0572 (mtt) REVERT: A 161 ILE cc_start: 0.8370 (tp) cc_final: 0.8028 (tt) REVERT: A 229 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7532 (mtm-85) REVERT: A 651 HIS cc_start: 0.7051 (OUTLIER) cc_final: 0.6010 (p-80) REVERT: A 713 MET cc_start: 0.8497 (mmt) cc_final: 0.7911 (mpp) REVERT: B 75 MET cc_start: 0.3470 (mpp) cc_final: 0.2894 (tpt) REVERT: B 183 ASN cc_start: 0.7509 (m-40) cc_final: 0.7243 (p0) REVERT: B 229 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7513 (mtm-85) REVERT: B 552 TRP cc_start: 0.7878 (t-100) cc_final: 0.4790 (m-10) REVERT: B 647 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.8352 (p0) REVERT: B 651 HIS cc_start: 0.7071 (OUTLIER) cc_final: 0.6204 (p-80) REVERT: B 787 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7601 (tm-30) outliers start: 27 outliers final: 18 residues processed: 162 average time/residue: 0.0973 time to fit residues: 24.2967 Evaluate side-chains 153 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 95 GLU 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 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 688 ILE Chi-restraints excluded: chain A residue 851 HIS 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 647 ASN Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 851 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 87 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.0060 chunk 59 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 159 optimal weight: 0.6980 chunk 151 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.149344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.116626 restraints weight = 15822.300| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.83 r_work: 0.3182 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2325 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= 0.125 Angle : 0.498 8.927 18206 Z= 0.260 Chirality : 0.038 0.133 2002 Planarity : 0.004 0.046 2292 Dihedral : 6.067 60.156 1890 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.80 % Allowed : 14.77 % Favored : 83.43 % 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: 2.11 (0.22), residues: 1604 helix: 2.66 (0.17), residues: 1002 sheet: -0.46 (0.41), residues: 174 loop : -0.91 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 199 TYR 0.009 0.001 TYR B 492 PHE 0.021 0.001 PHE A 397 TRP 0.005 0.001 TRP B 804 HIS 0.002 0.001 HIS B 578 Details of bonding type rmsd covalent geometry : bond 0.00270 (13404) covalent geometry : angle 0.49762 (18206) hydrogen bonds : bond 0.04922 ( 855) hydrogen bonds : angle 4.39729 ( 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 162 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.484 Fit side-chains REVERT: A 71 MET cc_start: 0.1697 (ttm) cc_final: 0.0591 (mtt) REVERT: A 161 ILE cc_start: 0.8412 (tp) cc_final: 0.8103 (tt) REVERT: A 229 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7540 (mtm-85) REVERT: A 238 MET cc_start: 0.8942 (ttp) cc_final: 0.8627 (ptm) REVERT: A 299 LYS cc_start: 0.8351 (mmtt) cc_final: 0.8095 (mmtt) REVERT: A 651 HIS cc_start: 0.7031 (OUTLIER) cc_final: 0.6061 (p-80) REVERT: A 713 MET cc_start: 0.8498 (mmt) cc_final: 0.7925 (mpp) REVERT: B 75 MET cc_start: 0.3435 (mpp) cc_final: 0.2893 (tpt) REVERT: B 183 ASN cc_start: 0.7469 (m-40) cc_final: 0.7198 (p0) REVERT: B 229 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7507 (mtm-85) REVERT: B 552 TRP cc_start: 0.7868 (t-100) cc_final: 0.4683 (m-10) REVERT: B 651 HIS cc_start: 0.7050 (OUTLIER) cc_final: 0.5862 (p-80) REVERT: B 667 MET cc_start: 0.8006 (tpp) cc_final: 0.7718 (tpt) REVERT: B 787 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7576 (tm-30) outliers start: 25 outliers final: 18 residues processed: 157 average time/residue: 0.1019 time to fit residues: 24.3536 Evaluate side-chains 153 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 435 ILE 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 851 HIS 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 851 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 7.9990 chunk 78 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 147 optimal weight: 0.0030 chunk 113 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 118 optimal weight: 0.0870 chunk 110 optimal weight: 0.4980 overall best weight: 0.4568 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.150753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.118169 restraints weight = 15744.505| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.92 r_work: 0.3178 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13404 Z= 0.113 Angle : 0.495 9.921 18206 Z= 0.258 Chirality : 0.037 0.150 2002 Planarity : 0.004 0.045 2292 Dihedral : 6.009 59.734 1890 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.66 % Allowed : 15.06 % Favored : 83.29 % 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: 2.71 (0.17), residues: 996 sheet: -0.44 (0.41), residues: 174 loop : -0.90 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 199 TYR 0.008 0.001 TYR A 492 PHE 0.028 0.001 PHE A 487 TRP 0.005 0.001 TRP B 804 HIS 0.002 0.000 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00233 (13404) covalent geometry : angle 0.49521 (18206) hydrogen bonds : bond 0.04656 ( 855) hydrogen bonds : angle 4.37688 ( 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 160 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.432 Fit side-chains REVERT: A 71 MET cc_start: 0.1684 (ttm) cc_final: 0.0580 (mtt) REVERT: A 161 ILE cc_start: 0.8385 (tp) cc_final: 0.8069 (tt) REVERT: A 229 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7545 (mtm-85) REVERT: A 299 LYS cc_start: 0.8352 (mmtt) cc_final: 0.8101 (mmtt) REVERT: A 651 HIS cc_start: 0.6972 (OUTLIER) cc_final: 0.5989 (p-80) REVERT: A 652 MET cc_start: 0.7762 (mmm) cc_final: 0.7479 (mmm) REVERT: A 713 MET cc_start: 0.8520 (mmt) cc_final: 0.7938 (mpp) REVERT: B 75 MET cc_start: 0.3622 (mpp) cc_final: 0.2967 (tpt) REVERT: B 183 ASN cc_start: 0.7487 (m-40) cc_final: 0.7222 (p0) REVERT: B 229 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7515 (mtm-85) REVERT: B 552 TRP cc_start: 0.7871 (t-100) cc_final: 0.4779 (m-10) REVERT: B 651 HIS cc_start: 0.7071 (OUTLIER) cc_final: 0.6025 (p-80) REVERT: B 667 MET cc_start: 0.7971 (tpp) cc_final: 0.7662 (tpt) outliers start: 23 outliers final: 18 residues processed: 157 average time/residue: 0.0998 time to fit residues: 24.1102 Evaluate side-chains 155 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 95 GLU 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 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 851 HIS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 ARG 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 851 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 24 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.148078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.115337 restraints weight = 15686.751| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.82 r_work: 0.3165 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13404 Z= 0.141 Angle : 0.520 9.073 18206 Z= 0.271 Chirality : 0.038 0.132 2002 Planarity : 0.004 0.046 2292 Dihedral : 6.044 59.529 1890 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.80 % Allowed : 15.06 % Favored : 83.14 % 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: 2.07 (0.22), residues: 1604 helix: 2.62 (0.17), residues: 1002 sheet: -0.46 (0.41), residues: 174 loop : -0.92 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 199 TYR 0.008 0.001 TYR B 239 PHE 0.021 0.001 PHE A 397 TRP 0.005 0.001 TRP B 804 HIS 0.003 0.001 HIS B 578 Details of bonding type rmsd covalent geometry : bond 0.00320 (13404) covalent geometry : angle 0.51974 (18206) hydrogen bonds : bond 0.05171 ( 855) hydrogen bonds : angle 4.42585 ( 2517) =============================================================================== Job complete usr+sys time: 3136.87 seconds wall clock time: 54 minutes 20.31 seconds (3260.31 seconds total)