Starting phenix.real_space_refine on Fri Jul 3 06:49:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7x06_32918/07_2026/7x06_32918.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x06_32918/07_2026/7x06_32918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7x06_32918/07_2026/7x06_32918.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7x06_32918/07_2026/7x06_32918.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x06_32918/07_2026/7x06_32918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x06_32918/07_2026/7x06_32918.map" model { file = "/net/cci-nas-00/data/ceres_data/7x06_32918/07_2026/7x06_32918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x06_32918/07_2026/7x06_32918.cif" } resolution = 3.1 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 P 4 5.49 5 Mg 2 5.21 5 S 72 5.16 5 C 8400 2.51 5 N 2156 2.21 5 O 2330 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: 12964 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6456 Classifications: {'peptide': 804} Link IDs: {'PTRANS': 30, 'TRANS': 773} Chain breaks: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 5.21, per 1000 atoms: 0.40 Number of scatterers: 12964 At special positions: 0 Unit cell: (114.49, 116.63, 128.4, 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) S 72 16.00 P 4 15.00 Mg 2 11.99 O 2330 8.00 N 2156 7.00 C 8400 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: 0.91 Conformation dependent library (CDL) restraints added in 419.8 milliseconds 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3024 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 4 sheets defined 65.8% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 67 through 74 Processing helix chain 'A' and resid 76 through 90 removed outlier: 3.506A 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 132 removed outlier: 4.263A pdb=" N GLU A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 162 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 263 removed outlier: 3.918A pdb=" N LEU A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN A 263 " --> pdb=" O TYR A 259 " (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: 3.591A pdb=" N HIS A 403 " --> pdb=" O PHE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 447 removed outlier: 3.532A pdb=" N SER A 427 " --> pdb=" O ASN A 423 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.537A pdb=" N ASN A 478 " --> pdb=" O PHE A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 485 through 490 Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 528 through 554 removed outlier: 3.556A pdb=" N LEU A 532 " --> pdb=" O ASP A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 564 through 587 removed outlier: 3.639A pdb=" N PHE A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 606 removed outlier: 3.524A pdb=" N GLN A 606 " --> pdb=" O GLN A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 647 removed outlier: 3.967A pdb=" N ASP A 623 " --> pdb=" O GLN A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 681 Processing helix chain 'A' and resid 684 through 706 removed outlier: 5.191A pdb=" N VAL A 697 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N TYR A 698 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N PHE A 699 " --> pdb=" O VAL A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 720 removed outlier: 5.146A pdb=" N THR A 716 " --> pdb=" O PHE A 712 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N HIS A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 720 " --> pdb=" O THR A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 736 Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 764 through 819 Processing helix chain 'A' and resid 824 through 857 removed outlier: 5.263A pdb=" N GLY A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU A 855 " --> pdb=" O HIS A 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 74 Processing helix chain 'B' and resid 76 through 90 removed outlier: 3.506A 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 132 removed outlier: 4.263A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 162 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 263 removed outlier: 3.918A pdb=" N LEU B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN B 263 " --> pdb=" O TYR B 259 " (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: 3.591A pdb=" N HIS B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 447 removed outlier: 3.533A pdb=" N SER B 427 " --> pdb=" O ASN B 423 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 474 Processing helix chain 'B' and resid 474 through 479 removed outlier: 3.536A pdb=" N ASN B 478 " --> pdb=" O PHE B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 485 Processing helix chain 'B' and resid 485 through 490 Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 528 through 554 removed outlier: 3.556A pdb=" N LEU B 532 " --> pdb=" O ASP B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 564 through 587 removed outlier: 3.638A pdb=" N PHE B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 606 removed outlier: 3.524A pdb=" N GLN B 606 " --> pdb=" O GLN B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 647 removed outlier: 3.968A pdb=" N ASP B 623 " --> pdb=" O GLN B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 681 Processing helix chain 'B' and resid 684 through 706 removed outlier: 5.190A pdb=" N VAL B 697 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N TYR B 698 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N PHE B 699 " --> pdb=" O VAL B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 720 removed outlier: 5.146A pdb=" N THR B 716 " --> pdb=" O PHE B 712 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N HIS B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 720 " --> pdb=" O THR B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 736 Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 764 through 819 Processing helix chain 'B' and resid 824 through 857 removed outlier: 5.263A pdb=" N GLY B 854 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU B 855 " --> pdb=" O HIS B 851 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56 removed outlier: 6.118A pdb=" N HIS B 175 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ARG B 200 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N THR B 332 " --> pdb=" O ARG B 200 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN B 346 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS B 352 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU B 232 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N CYS B 287 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE B 234 " --> pdb=" O CYS B 287 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL B 289 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE B 236 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N MET B 233 " --> pdb=" O ALA B 379 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N MET B 381 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N CYS B 235 " --> pdb=" O MET B 381 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG B 461 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLY B 406 " --> pdb=" O ARG B 461 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N HIS B 514 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA B 408 " --> pdb=" O HIS B 514 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL B 516 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLY B 410 " --> pdb=" O VAL B 516 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASP B 518 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N LEU B 412 " --> pdb=" O ASP B 518 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N VAL B 520 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 9.449A pdb=" N VAL B 414 " --> pdb=" O VAL B 520 " (cutoff:3.500A) removed outlier: 6.915A 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: 7.574A pdb=" N HIS A 514 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA A 408 " --> pdb=" O HIS A 514 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A 516 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLY A 410 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ASP A 518 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N LEU A 412 " --> pdb=" O ASP A 518 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N VAL A 520 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 9.448A pdb=" N VAL A 414 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ARG A 522 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLY A 406 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG A 461 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N MET A 233 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N MET A 381 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N CYS A 235 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU A 232 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N CYS A 287 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE A 234 " --> pdb=" O CYS A 287 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL A 289 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE A 236 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLN A 346 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS A 352 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N THR A 332 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ARG A 200 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N HIS A 175 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL A 174 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N SER B 55 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.170A 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 337 840 hydrogen bonds defined for protein. 2472 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: 1.62 Time building geometry restraints manager: 1.22 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: 4075 1.34 - 1.46: 2257 1.46 - 1.57: 6862 1.57 - 1.69: 6 1.69 - 1.81: 112 Bond restraints: 13312 Sorted by residual: bond pdb=" O1B UDP B1001 " pdb=" PB UDP B1001 " ideal model delta sigma weight residual 1.530 1.491 0.039 1.00e-02 1.00e+04 1.56e+01 bond pdb=" O1B UDP A1001 " pdb=" PB UDP A1001 " ideal model delta sigma weight residual 1.530 1.491 0.039 1.00e-02 1.00e+04 1.54e+01 bond pdb=" C TYR B 462 " pdb=" N GLU B 463 " ideal model delta sigma weight residual 1.332 1.311 0.021 1.40e-02 5.10e+03 2.33e+00 bond pdb=" C TYR A 462 " pdb=" N GLU A 463 " ideal model delta sigma weight residual 1.332 1.311 0.021 1.40e-02 5.10e+03 2.23e+00 bond pdb=" C ASN B 541 " pdb=" O ASN B 541 " ideal model delta sigma weight residual 1.236 1.249 -0.012 1.15e-02 7.56e+03 1.17e+00 ... (remaining 13307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 17876 1.82 - 3.64: 166 3.64 - 5.46: 32 5.46 - 7.28: 2 7.28 - 9.10: 6 Bond angle restraints: 18082 Sorted by residual: angle pdb=" O1B UDP B1001 " pdb=" PB UDP B1001 " pdb=" O3A UDP B1001 " ideal model delta sigma weight residual 102.95 112.05 -9.10 1.00e+00 1.00e+00 8.28e+01 angle pdb=" O1B UDP A1001 " pdb=" PB UDP A1001 " pdb=" O3A UDP A1001 " ideal model delta sigma weight residual 102.95 112.01 -9.06 1.00e+00 1.00e+00 8.22e+01 angle pdb=" O3A UDP A1001 " pdb=" PB UDP A1001 " pdb=" O3B UDP A1001 " ideal model delta sigma weight residual 112.01 103.00 9.01 1.00e+00 1.00e+00 8.11e+01 angle pdb=" O3A UDP B1001 " pdb=" PB UDP B1001 " pdb=" O3B UDP B1001 " ideal model delta sigma weight residual 112.01 103.02 8.99 1.00e+00 1.00e+00 8.08e+01 angle pdb=" N CYS A 47 " pdb=" CA CYS A 47 " pdb=" C CYS A 47 " ideal model delta sigma weight residual 114.04 110.73 3.31 1.24e+00 6.50e-01 7.12e+00 ... (remaining 18077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 7293 16.48 - 32.96: 391 32.96 - 49.44: 56 49.44 - 65.92: 10 65.92 - 82.40: 4 Dihedral angle restraints: 7754 sinusoidal: 3044 harmonic: 4710 Sorted by residual: dihedral pdb=" CA GLY A 455 " pdb=" C GLY A 455 " pdb=" N ALA A 456 " pdb=" CA ALA A 456 " ideal model delta harmonic sigma weight residual 180.00 154.85 25.15 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA GLY B 455 " pdb=" C GLY B 455 " pdb=" N ALA B 456 " pdb=" CA ALA B 456 " ideal model delta harmonic sigma weight residual 180.00 154.89 25.11 0 5.00e+00 4.00e-02 2.52e+01 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 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 7751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1141 0.026 - 0.052: 541 0.052 - 0.078: 187 0.078 - 0.103: 78 0.103 - 0.129: 37 Chirality restraints: 1984 Sorted by residual: chirality pdb=" CA ILE A 288 " pdb=" N ILE A 288 " pdb=" C ILE A 288 " pdb=" CB ILE A 288 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE B 288 " pdb=" N ILE B 288 " pdb=" C ILE B 288 " pdb=" CB ILE B 288 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA PHE A 545 " pdb=" N PHE A 545 " pdb=" C PHE A 545 " pdb=" CB PHE A 545 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 1981 not shown) Planarity restraints: 2282 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 598 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.86e+00 pdb=" C PHE B 598 " -0.045 2.00e-02 2.50e+03 pdb=" O PHE B 598 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE B 599 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 598 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.72e+00 pdb=" C PHE A 598 " 0.045 2.00e-02 2.50e+03 pdb=" O PHE A 598 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE A 599 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 599 " 0.012 2.00e-02 2.50e+03 2.29e-02 5.23e+00 pdb=" C ILE B 599 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE B 599 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL B 600 " 0.013 2.00e-02 2.50e+03 ... (remaining 2279 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1793 2.75 - 3.29: 11900 3.29 - 3.83: 21058 3.83 - 4.36: 22952 4.36 - 4.90: 43374 Nonbonded interactions: 101077 Sorted by model distance: nonbonded pdb=" OH TYR A 52 " pdb=" OE2 GLU B 225 " model vdw 2.215 3.040 nonbonded pdb=" OE2 GLU A 225 " pdb=" OH TYR B 52 " model vdw 2.228 3.040 nonbonded pdb=" OE1 GLU A 312 " pdb=" NH2 ARG B 773 " model vdw 2.292 3.120 nonbonded pdb=" OG SER A 93 " pdb=" O LYS B 762 " model vdw 2.315 3.040 nonbonded pdb=" NH2 ARG A 773 " pdb=" OE1 GLU B 312 " model vdw 2.318 3.120 ... (remaining 101072 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: 1.530 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.630 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:0.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13312 Z= 0.149 Angle : 0.508 9.098 18082 Z= 0.297 Chirality : 0.038 0.129 1984 Planarity : 0.004 0.027 2282 Dihedral : 10.343 82.402 4730 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.43 % Allowed : 4.62 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.22), residues: 1600 helix: 2.76 (0.17), residues: 966 sheet: -0.19 (0.40), residues: 170 loop : -1.14 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 293 TYR 0.013 0.001 TYR B 473 PHE 0.012 0.001 PHE B 545 TRP 0.008 0.001 TRP A 804 HIS 0.003 0.001 HIS B 709 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 (13312) covalent geometry : angle 0.50784 / 0.30 (18082) hydrogen bonds : bond 0.11361 / 7.52 ( 840) hydrogen bonds : angle 5.13100 / 3.80 ( 2472) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 218 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.2935 (mmm) cc_final: 0.2594 (mmp) REVERT: A 115 ASP cc_start: 0.6876 (m-30) cc_final: 0.6486 (t0) REVERT: A 299 LYS cc_start: 0.8092 (mmtt) cc_final: 0.7856 (mmtm) REVERT: A 382 ASP cc_start: 0.8246 (m-30) cc_final: 0.8002 (m-30) REVERT: A 552 TRP cc_start: 0.7281 (OUTLIER) cc_final: 0.5862 (t-100) REVERT: A 736 ASN cc_start: 0.7915 (m110) cc_final: 0.7454 (m-40) REVERT: A 850 ILE cc_start: 0.8154 (tt) cc_final: 0.7931 (tt) REVERT: B 75 MET cc_start: 0.3368 (mmm) cc_final: 0.2863 (mmt) REVERT: B 382 ASP cc_start: 0.8229 (m-30) cc_final: 0.7944 (m-30) REVERT: B 451 SER cc_start: 0.8111 (m) cc_final: 0.7896 (p) REVERT: B 475 GLN cc_start: 0.8097 (tt0) cc_final: 0.7849 (tt0) REVERT: B 552 TRP cc_start: 0.7292 (OUTLIER) cc_final: 0.5859 (t-100) REVERT: B 652 MET cc_start: 0.6940 (mmm) cc_final: 0.6667 (mmm) REVERT: B 736 ASN cc_start: 0.8051 (m110) cc_final: 0.7604 (m-40) REVERT: B 790 LYS cc_start: 0.7762 (mmtt) cc_final: 0.7485 (mptt) REVERT: B 797 ARG cc_start: 0.7567 (ppt-90) cc_final: 0.7337 (ptt90) REVERT: B 850 ILE cc_start: 0.8088 (tt) cc_final: 0.7874 (tt) outliers start: 6 outliers final: 2 residues processed: 222 average time/residue: 0.1076 time to fit residues: 33.9796 Evaluate side-chains 149 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 145 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 552 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 295 GLN B 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.133183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.101216 restraints weight = 15501.280| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.27 r_work: 0.3033 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13312 Z= 0.215 Angle : 0.575 9.658 18082 Z= 0.303 Chirality : 0.041 0.142 1984 Planarity : 0.004 0.032 2282 Dihedral : 4.567 48.493 1770 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.81 % Allowed : 9.10 % Favored : 89.09 % 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: 1.61 (0.21), residues: 1600 helix: 2.30 (0.16), residues: 982 sheet: -0.37 (0.40), residues: 172 loop : -1.20 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 103 TYR 0.019 0.002 TYR A 492 PHE 0.017 0.002 PHE B 329 TRP 0.008 0.001 TRP A 804 HIS 0.004 0.001 HIS A 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.21 (13312) covalent geometry : angle 0.57469 / 0.30 (18082) hydrogen bonds : bond 0.06637 / 4.51 ( 840) hydrogen bonds : angle 4.77266 / 3.54 ( 2472) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.2284 (mmm) cc_final: 0.1949 (mmp) REVERT: A 95 GLU cc_start: 0.7125 (tp30) cc_final: 0.6640 (tp30) REVERT: A 115 ASP cc_start: 0.7543 (m-30) cc_final: 0.7003 (t0) REVERT: A 244 GLN cc_start: 0.7670 (tp40) cc_final: 0.7395 (pm20) REVERT: A 299 LYS cc_start: 0.8061 (mmtt) cc_final: 0.7798 (mmtm) REVERT: A 552 TRP cc_start: 0.7809 (OUTLIER) cc_final: 0.6388 (t-100) REVERT: A 730 THR cc_start: 0.8940 (m) cc_final: 0.8566 (p) REVERT: A 736 ASN cc_start: 0.8596 (m110) cc_final: 0.7873 (m-40) REVERT: A 850 ILE cc_start: 0.8157 (tt) cc_final: 0.7821 (tt) REVERT: B 71 MET cc_start: 0.5016 (mtt) cc_final: 0.4757 (ttm) REVERT: B 75 MET cc_start: 0.2765 (mmm) cc_final: 0.2326 (mmt) REVERT: B 244 GLN cc_start: 0.7629 (tp40) cc_final: 0.7387 (pm20) REVERT: B 475 GLN cc_start: 0.8066 (tt0) cc_final: 0.7864 (tt0) REVERT: B 552 TRP cc_start: 0.7795 (OUTLIER) cc_final: 0.6349 (t-100) REVERT: B 652 MET cc_start: 0.7209 (mmm) cc_final: 0.6928 (mmm) REVERT: B 730 THR cc_start: 0.9037 (m) cc_final: 0.8786 (p) REVERT: B 736 ASN cc_start: 0.8516 (m110) cc_final: 0.7586 (m-40) REVERT: B 790 LYS cc_start: 0.7832 (mmtt) cc_final: 0.7434 (mptt) REVERT: B 797 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7871 (ptt90) REVERT: B 850 ILE cc_start: 0.8185 (tt) cc_final: 0.7852 (tt) outliers start: 25 outliers final: 17 residues processed: 169 average time/residue: 0.0929 time to fit residues: 24.2016 Evaluate side-chains 163 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 552 TRP Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 792 ASN Chi-restraints excluded: chain B residue 797 ARG Chi-restraints excluded: chain B residue 852 THR 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 60 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN B 256 ASN B 295 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.145229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.114191 restraints weight = 15288.175| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.16 r_work: 0.3029 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13312 Z= 0.130 Angle : 0.487 6.807 18082 Z= 0.259 Chirality : 0.038 0.128 1984 Planarity : 0.004 0.031 2282 Dihedral : 4.413 48.834 1768 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.24 % Allowed : 10.26 % Favored : 87.50 % 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: 1.79 (0.22), residues: 1600 helix: 2.48 (0.16), residues: 982 sheet: -0.58 (0.41), residues: 156 loop : -1.09 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 164 TYR 0.020 0.001 TYR B 732 PHE 0.013 0.001 PHE A 601 TRP 0.005 0.001 TRP A 804 HIS 0.002 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (13312) covalent geometry : angle 0.48724 / 0.26 (18082) hydrogen bonds : bond 0.05567 / 3.80 ( 840) hydrogen bonds : angle 4.57762 / 3.40 ( 2472) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.5031 (OUTLIER) cc_final: 0.4642 (mtt) REVERT: A 75 MET cc_start: 0.2246 (mmm) cc_final: 0.1936 (mmp) REVERT: A 95 GLU cc_start: 0.6976 (tp30) cc_final: 0.6418 (tp30) REVERT: A 115 ASP cc_start: 0.7422 (m-30) cc_final: 0.6792 (t0) REVERT: A 299 LYS cc_start: 0.7761 (mmtt) cc_final: 0.7543 (mmtm) REVERT: A 552 TRP cc_start: 0.7623 (OUTLIER) cc_final: 0.6190 (t-100) REVERT: A 652 MET cc_start: 0.6630 (mmm) cc_final: 0.6376 (mmm) REVERT: A 730 THR cc_start: 0.8684 (m) cc_final: 0.8275 (p) REVERT: A 736 ASN cc_start: 0.8437 (m110) cc_final: 0.7582 (m-40) REVERT: A 850 ILE cc_start: 0.7901 (tt) cc_final: 0.7603 (tt) REVERT: B 71 MET cc_start: 0.5081 (mtt) cc_final: 0.4862 (ttm) REVERT: B 75 MET cc_start: 0.2630 (mmm) cc_final: 0.2229 (mmp) REVERT: B 95 GLU cc_start: 0.6808 (tp30) cc_final: 0.6508 (tp30) REVERT: B 552 TRP cc_start: 0.7546 (OUTLIER) cc_final: 0.6082 (t-100) REVERT: B 652 MET cc_start: 0.6898 (mmm) cc_final: 0.6582 (mmm) REVERT: B 713 MET cc_start: 0.8658 (mmm) cc_final: 0.8454 (mmm) REVERT: B 730 THR cc_start: 0.8697 (m) cc_final: 0.8325 (p) REVERT: B 736 ASN cc_start: 0.8505 (m110) cc_final: 0.7498 (m-40) REVERT: B 790 LYS cc_start: 0.7656 (mmtt) cc_final: 0.7254 (mptt) REVERT: B 850 ILE cc_start: 0.7889 (tt) cc_final: 0.7592 (tt) outliers start: 31 outliers final: 17 residues processed: 162 average time/residue: 0.0861 time to fit residues: 21.5079 Evaluate side-chains 156 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 552 TRP Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 837 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 106 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 23 optimal weight: 0.0970 chunk 48 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 295 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.139292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.108729 restraints weight = 15334.910| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.13 r_work: 0.2974 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13312 Z= 0.206 Angle : 0.551 7.718 18082 Z= 0.293 Chirality : 0.041 0.142 1984 Planarity : 0.004 0.032 2282 Dihedral : 4.538 48.942 1768 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.60 % Allowed : 11.13 % Favored : 86.27 % 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: 1.59 (0.22), residues: 1600 helix: 2.25 (0.16), residues: 988 sheet: -0.52 (0.40), residues: 176 loop : -1.10 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 164 TYR 0.020 0.002 TYR B 732 PHE 0.017 0.002 PHE A 545 TRP 0.007 0.001 TRP B 511 HIS 0.004 0.001 HIS B 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 (13312) covalent geometry : angle 0.55065 / 0.29 (18082) hydrogen bonds : bond 0.06651 / 4.52 ( 840) hydrogen bonds : angle 4.67904 / 3.47 ( 2472) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.4935 (OUTLIER) cc_final: 0.4566 (mtt) REVERT: A 75 MET cc_start: 0.2294 (mmm) cc_final: 0.1954 (mmp) REVERT: A 95 GLU cc_start: 0.7074 (tp30) cc_final: 0.6499 (tp30) REVERT: A 115 ASP cc_start: 0.7541 (m-30) cc_final: 0.6930 (t0) REVERT: A 244 GLN cc_start: 0.7563 (tp40) cc_final: 0.7216 (pm20) REVERT: A 299 LYS cc_start: 0.7696 (mmtt) cc_final: 0.7460 (mmtm) REVERT: A 552 TRP cc_start: 0.7673 (OUTLIER) cc_final: 0.6274 (t-100) REVERT: A 730 THR cc_start: 0.8802 (m) cc_final: 0.8461 (p) REVERT: A 736 ASN cc_start: 0.8624 (m110) cc_final: 0.7833 (m-40) REVERT: A 850 ILE cc_start: 0.8023 (tt) cc_final: 0.7718 (tt) REVERT: B 95 GLU cc_start: 0.6950 (tp30) cc_final: 0.6407 (tp30) REVERT: B 244 GLN cc_start: 0.7552 (tp40) cc_final: 0.7229 (pm20) REVERT: B 552 TRP cc_start: 0.7646 (OUTLIER) cc_final: 0.6214 (t-100) REVERT: B 652 MET cc_start: 0.7003 (mmm) cc_final: 0.6708 (mmm) REVERT: B 730 THR cc_start: 0.8825 (m) cc_final: 0.8495 (p) REVERT: B 736 ASN cc_start: 0.8668 (m110) cc_final: 0.7863 (m-40) REVERT: B 790 LYS cc_start: 0.7650 (mmtt) cc_final: 0.7239 (mptt) REVERT: B 850 ILE cc_start: 0.8030 (tt) cc_final: 0.7727 (tt) outliers start: 36 outliers final: 27 residues processed: 164 average time/residue: 0.0880 time to fit residues: 22.0168 Evaluate side-chains 167 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 552 TRP Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 792 ASN Chi-restraints excluded: chain B residue 797 ARG Chi-restraints excluded: chain B residue 837 THR 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 106 optimal weight: 0.0030 chunk 32 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.142644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.112057 restraints weight = 15269.868| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.14 r_work: 0.3040 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13312 Z= 0.145 Angle : 0.497 6.796 18082 Z= 0.265 Chirality : 0.038 0.131 1984 Planarity : 0.004 0.031 2282 Dihedral : 4.441 49.455 1768 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.46 % Allowed : 12.21 % Favored : 85.33 % 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: 1.70 (0.22), residues: 1600 helix: 2.37 (0.16), residues: 988 sheet: -0.50 (0.40), residues: 176 loop : -1.13 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 164 TYR 0.015 0.001 TYR B 732 PHE 0.014 0.001 PHE B 545 TRP 0.005 0.001 TRP B 511 HIS 0.004 0.001 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (13312) covalent geometry : angle 0.49716 / 0.27 (18082) hydrogen bonds : bond 0.05871 / 4.00 ( 840) hydrogen bonds : angle 4.57925 / 3.40 ( 2472) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.5031 (OUTLIER) cc_final: 0.4661 (mtt) REVERT: A 75 MET cc_start: 0.2435 (mmm) cc_final: 0.2060 (mmp) REVERT: A 95 GLU cc_start: 0.7082 (tp30) cc_final: 0.6512 (tp30) REVERT: A 115 ASP cc_start: 0.7502 (m-30) cc_final: 0.6961 (t0) REVERT: A 244 GLN cc_start: 0.7555 (tp40) cc_final: 0.7334 (pm20) REVERT: A 299 LYS cc_start: 0.7865 (mmtt) cc_final: 0.7635 (mmtm) REVERT: A 552 TRP cc_start: 0.7737 (OUTLIER) cc_final: 0.6340 (t-100) REVERT: A 652 MET cc_start: 0.6861 (mmm) cc_final: 0.6654 (mmm) REVERT: A 730 THR cc_start: 0.8896 (m) cc_final: 0.8534 (p) REVERT: A 736 ASN cc_start: 0.8606 (m110) cc_final: 0.7861 (m-40) REVERT: A 850 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7803 (tt) REVERT: B 95 GLU cc_start: 0.6977 (tp30) cc_final: 0.6661 (tp30) REVERT: B 244 GLN cc_start: 0.7500 (tp40) cc_final: 0.7286 (pm20) REVERT: B 552 TRP cc_start: 0.7708 (OUTLIER) cc_final: 0.6273 (t-100) REVERT: B 652 MET cc_start: 0.6950 (mmm) cc_final: 0.6699 (mmm) REVERT: B 713 MET cc_start: 0.8884 (mmm) cc_final: 0.8683 (mmm) REVERT: B 730 THR cc_start: 0.8899 (m) cc_final: 0.8539 (p) REVERT: B 736 ASN cc_start: 0.8696 (m110) cc_final: 0.7884 (m-40) REVERT: B 790 LYS cc_start: 0.7763 (mmtt) cc_final: 0.7330 (mptt) REVERT: B 850 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7818 (tt) outliers start: 34 outliers final: 24 residues processed: 165 average time/residue: 0.0880 time to fit residues: 22.2148 Evaluate side-chains 166 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 552 TRP Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 797 ARG Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 76 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 85 optimal weight: 0.0370 chunk 46 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 295 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.140816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.109726 restraints weight = 15258.301| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.21 r_work: 0.3007 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13312 Z= 0.138 Angle : 0.488 6.812 18082 Z= 0.259 Chirality : 0.038 0.132 1984 Planarity : 0.004 0.030 2282 Dihedral : 4.352 49.326 1768 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.53 % Allowed : 12.64 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.79 (0.22), residues: 1600 helix: 2.44 (0.16), residues: 988 sheet: -0.50 (0.40), residues: 176 loop : -1.08 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 164 TYR 0.013 0.001 TYR B 732 PHE 0.014 0.001 PHE A 601 TRP 0.005 0.001 TRP B 202 HIS 0.004 0.001 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (13312) covalent geometry : angle 0.48763 / 0.26 (18082) hydrogen bonds : bond 0.05623 / 3.84 ( 840) hydrogen bonds : angle 4.52142 / 3.35 ( 2472) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.2238 (mmm) cc_final: 0.1890 (mmp) REVERT: A 95 GLU cc_start: 0.7083 (tp30) cc_final: 0.6492 (tp30) REVERT: A 115 ASP cc_start: 0.7437 (m-30) cc_final: 0.6865 (t0) REVERT: A 244 GLN cc_start: 0.7442 (tp40) cc_final: 0.7197 (pm20) REVERT: A 299 LYS cc_start: 0.7712 (mmtt) cc_final: 0.7478 (mmtm) REVERT: A 318 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.8534 (m-40) REVERT: A 552 TRP cc_start: 0.7685 (OUTLIER) cc_final: 0.6310 (t-100) REVERT: A 652 MET cc_start: 0.6763 (mmm) cc_final: 0.6534 (mmm) REVERT: A 730 THR cc_start: 0.8785 (m) cc_final: 0.8417 (p) REVERT: A 736 ASN cc_start: 0.8657 (m110) cc_final: 0.7833 (m-40) REVERT: A 850 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7690 (tt) REVERT: B 95 GLU cc_start: 0.6979 (tp30) cc_final: 0.6483 (tp30) REVERT: B 295 GLN cc_start: 0.7807 (mm110) cc_final: 0.7189 (mm-40) REVERT: B 325 GLN cc_start: 0.8515 (mm-40) cc_final: 0.8206 (mp10) REVERT: B 552 TRP cc_start: 0.7616 (OUTLIER) cc_final: 0.6192 (t-100) REVERT: B 652 MET cc_start: 0.6774 (mmm) cc_final: 0.6512 (mmm) REVERT: B 730 THR cc_start: 0.8883 (m) cc_final: 0.8597 (p) REVERT: B 736 ASN cc_start: 0.8664 (m110) cc_final: 0.7859 (m-40) REVERT: B 790 LYS cc_start: 0.7600 (mmtt) cc_final: 0.7190 (mptt) REVERT: B 850 ILE cc_start: 0.8001 (tt) cc_final: 0.7695 (tt) outliers start: 35 outliers final: 29 residues processed: 166 average time/residue: 0.0860 time to fit residues: 21.9922 Evaluate side-chains 167 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 552 TRP Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 797 ARG Chi-restraints excluded: chain B residue 837 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 109 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 82 optimal weight: 0.0870 chunk 112 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.134612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.102772 restraints weight = 15612.119| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.28 r_work: 0.3159 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13312 Z= 0.128 Angle : 0.479 6.597 18082 Z= 0.255 Chirality : 0.038 0.130 1984 Planarity : 0.004 0.030 2282 Dihedral : 4.303 49.251 1768 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.82 % Allowed : 12.57 % Favored : 84.61 % 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: 1.83 (0.22), residues: 1600 helix: 2.49 (0.16), residues: 988 sheet: -0.38 (0.40), residues: 174 loop : -1.18 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 164 TYR 0.013 0.001 TYR B 732 PHE 0.013 0.001 PHE A 601 TRP 0.005 0.001 TRP B 202 HIS 0.004 0.001 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (13312) covalent geometry : angle 0.47943 / 0.25 (18082) hydrogen bonds : bond 0.05411 / 3.69 ( 840) hydrogen bonds : angle 4.48490 / 3.32 ( 2472) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.5097 (OUTLIER) cc_final: 0.4884 (mtt) REVERT: A 75 MET cc_start: 0.2439 (mmm) cc_final: 0.2062 (mmp) REVERT: A 95 GLU cc_start: 0.7140 (tp30) cc_final: 0.6632 (tp30) REVERT: A 115 ASP cc_start: 0.7529 (m-30) cc_final: 0.7039 (t0) REVERT: A 299 LYS cc_start: 0.7936 (mmtt) cc_final: 0.7719 (mmtm) REVERT: A 325 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8387 (mp10) REVERT: A 510 ASN cc_start: 0.9090 (OUTLIER) cc_final: 0.8883 (p0) REVERT: A 552 TRP cc_start: 0.7853 (OUTLIER) cc_final: 0.6501 (t-100) REVERT: A 730 THR cc_start: 0.8945 (m) cc_final: 0.8591 (p) REVERT: A 736 ASN cc_start: 0.8704 (m110) cc_final: 0.7931 (m-40) REVERT: A 850 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7844 (tt) REVERT: B 95 GLU cc_start: 0.7114 (tp30) cc_final: 0.6628 (tp30) REVERT: B 295 GLN cc_start: 0.7923 (mm110) cc_final: 0.7366 (mm-40) REVERT: B 325 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8377 (mp10) REVERT: B 552 TRP cc_start: 0.7770 (OUTLIER) cc_final: 0.6356 (t-100) REVERT: B 652 MET cc_start: 0.6942 (mmm) cc_final: 0.6726 (mmm) REVERT: B 730 THR cc_start: 0.9029 (m) cc_final: 0.8754 (p) REVERT: B 736 ASN cc_start: 0.8719 (m110) cc_final: 0.7973 (m-40) REVERT: B 790 LYS cc_start: 0.7756 (mmtt) cc_final: 0.7356 (mptt) REVERT: B 850 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7839 (tt) outliers start: 39 outliers final: 28 residues processed: 163 average time/residue: 0.0842 time to fit residues: 21.0798 Evaluate side-chains 166 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 552 TRP Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 792 ASN Chi-restraints excluded: chain B residue 797 ARG Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 141 optimal weight: 0.0770 chunk 95 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 0.0030 chunk 106 optimal weight: 0.4980 overall best weight: 0.9152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.133631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.101850 restraints weight = 15593.019| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.28 r_work: 0.3148 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13312 Z= 0.144 Angle : 0.493 6.829 18082 Z= 0.262 Chirality : 0.038 0.134 1984 Planarity : 0.004 0.029 2282 Dihedral : 4.310 49.273 1768 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.96 % Allowed : 12.86 % Favored : 84.18 % 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: 1.80 (0.22), residues: 1600 helix: 2.47 (0.16), residues: 988 sheet: -0.44 (0.40), residues: 176 loop : -1.15 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 164 TYR 0.015 0.001 TYR A 732 PHE 0.013 0.001 PHE B 601 TRP 0.006 0.001 TRP B 511 HIS 0.004 0.001 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (13312) covalent geometry : angle 0.49349 / 0.26 (18082) hydrogen bonds : bond 0.05647 / 3.85 ( 840) hydrogen bonds : angle 4.49899 / 3.33 ( 2472) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.2380 (mmm) cc_final: 0.1998 (mmp) REVERT: A 95 GLU cc_start: 0.7181 (tp30) cc_final: 0.6656 (tp30) REVERT: A 115 ASP cc_start: 0.7533 (m-30) cc_final: 0.7055 (t0) REVERT: A 244 GLN cc_start: 0.7597 (tp40) cc_final: 0.7384 (pm20) REVERT: A 299 LYS cc_start: 0.7949 (mmtt) cc_final: 0.7726 (mmtm) REVERT: A 318 ASN cc_start: 0.8946 (OUTLIER) cc_final: 0.8706 (m-40) REVERT: A 552 TRP cc_start: 0.7875 (OUTLIER) cc_final: 0.6538 (t-100) REVERT: A 730 THR cc_start: 0.8958 (m) cc_final: 0.8604 (p) REVERT: A 736 ASN cc_start: 0.8736 (m110) cc_final: 0.7964 (m-40) REVERT: A 850 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7816 (tt) REVERT: B 95 GLU cc_start: 0.7155 (tp30) cc_final: 0.6663 (tp30) REVERT: B 244 GLN cc_start: 0.7596 (tp40) cc_final: 0.7393 (pm20) REVERT: B 295 GLN cc_start: 0.7892 (mm110) cc_final: 0.7330 (mm-40) REVERT: B 325 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8424 (mp10) REVERT: B 552 TRP cc_start: 0.7803 (OUTLIER) cc_final: 0.6404 (t-100) REVERT: B 563 HIS cc_start: 0.8869 (OUTLIER) cc_final: 0.8008 (m90) REVERT: B 652 MET cc_start: 0.6982 (mmm) cc_final: 0.6772 (mmm) REVERT: B 730 THR cc_start: 0.9043 (m) cc_final: 0.8767 (p) REVERT: B 736 ASN cc_start: 0.8797 (OUTLIER) cc_final: 0.8055 (m-40) REVERT: B 790 LYS cc_start: 0.7763 (mmtt) cc_final: 0.7366 (mptt) REVERT: B 850 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7784 (tt) outliers start: 41 outliers final: 32 residues processed: 166 average time/residue: 0.0877 time to fit residues: 22.1906 Evaluate side-chains 174 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 552 TRP Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 792 ASN Chi-restraints excluded: chain B residue 797 ARG Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 78 optimal weight: 1.9990 chunk 47 optimal weight: 0.0980 chunk 131 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 82 optimal weight: 0.0050 chunk 83 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 510 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.136970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.105256 restraints weight = 15548.200| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.27 r_work: 0.3041 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13312 Z= 0.109 Angle : 0.465 6.228 18082 Z= 0.247 Chirality : 0.037 0.124 1984 Planarity : 0.004 0.029 2282 Dihedral : 4.215 49.369 1768 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.53 % Allowed : 13.51 % Favored : 83.96 % 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: 1600 helix: 2.65 (0.17), residues: 984 sheet: -0.26 (0.41), residues: 172 loop : -1.10 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 164 TYR 0.014 0.001 TYR A 732 PHE 0.013 0.001 PHE A 601 TRP 0.005 0.001 TRP B 202 HIS 0.003 0.001 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.11 (13312) covalent geometry : angle 0.46503 / 0.25 (18082) hydrogen bonds : bond 0.04917 / 3.36 ( 840) hydrogen bonds : angle 4.42340 / 3.27 ( 2472) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.2231 (mmm) cc_final: 0.1897 (mmp) REVERT: A 95 GLU cc_start: 0.7027 (tp30) cc_final: 0.6514 (tp30) REVERT: A 115 ASP cc_start: 0.7412 (m-30) cc_final: 0.6858 (t0) REVERT: A 299 LYS cc_start: 0.7710 (mmtt) cc_final: 0.7498 (mmtm) REVERT: A 325 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8239 (mp10) REVERT: A 510 ASN cc_start: 0.8996 (OUTLIER) cc_final: 0.8796 (p0) REVERT: A 552 TRP cc_start: 0.7597 (OUTLIER) cc_final: 0.6283 (t-100) REVERT: A 563 HIS cc_start: 0.8773 (OUTLIER) cc_final: 0.7863 (m90) REVERT: A 730 THR cc_start: 0.8766 (m) cc_final: 0.8385 (p) REVERT: A 736 ASN cc_start: 0.8659 (m110) cc_final: 0.7816 (m-40) REVERT: A 850 ILE cc_start: 0.7997 (tt) cc_final: 0.7693 (tt) REVERT: B 95 GLU cc_start: 0.6980 (tp30) cc_final: 0.6671 (tp30) REVERT: B 295 GLN cc_start: 0.7787 (mm110) cc_final: 0.7160 (mm-40) REVERT: B 552 TRP cc_start: 0.7521 (OUTLIER) cc_final: 0.6112 (t-100) REVERT: B 563 HIS cc_start: 0.8771 (OUTLIER) cc_final: 0.7855 (m90) REVERT: B 730 THR cc_start: 0.8872 (m) cc_final: 0.8579 (p) REVERT: B 736 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.7915 (m-40) REVERT: B 790 LYS cc_start: 0.7589 (mmtt) cc_final: 0.7187 (mptt) REVERT: B 850 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7610 (tt) outliers start: 35 outliers final: 25 residues processed: 161 average time/residue: 0.0918 time to fit residues: 22.4706 Evaluate side-chains 164 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 552 TRP Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 712 PHE Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 797 ARG Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 115 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 80 optimal weight: 0.0270 chunk 68 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 118 optimal weight: 0.0270 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 510 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.135924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.104192 restraints weight = 15640.100| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.26 r_work: 0.3034 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13312 Z= 0.118 Angle : 0.475 6.453 18082 Z= 0.251 Chirality : 0.037 0.129 1984 Planarity : 0.004 0.029 2282 Dihedral : 4.187 49.090 1768 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.38 % Allowed : 13.51 % Favored : 84.10 % 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: 1600 helix: 2.69 (0.17), residues: 980 sheet: -0.26 (0.41), residues: 172 loop : -1.15 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 164 TYR 0.015 0.001 TYR B 125 PHE 0.014 0.001 PHE B 601 TRP 0.005 0.001 TRP B 202 HIS 0.004 0.001 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (13312) covalent geometry : angle 0.47549 / 0.25 (18082) hydrogen bonds : bond 0.05045 / 3.45 ( 840) hydrogen bonds : angle 4.41116 / 3.26 ( 2472) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.2252 (mmm) cc_final: 0.1913 (mmp) REVERT: A 95 GLU cc_start: 0.7107 (tp30) cc_final: 0.6754 (tp30) REVERT: A 115 ASP cc_start: 0.7409 (m-30) cc_final: 0.6865 (t0) REVERT: A 299 LYS cc_start: 0.7692 (mmtt) cc_final: 0.7475 (mmtm) REVERT: A 325 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8182 (mp10) REVERT: A 510 ASN cc_start: 0.9006 (OUTLIER) cc_final: 0.8797 (p0) REVERT: A 552 TRP cc_start: 0.7575 (OUTLIER) cc_final: 0.6259 (t-100) REVERT: A 563 HIS cc_start: 0.8766 (OUTLIER) cc_final: 0.7850 (m90) REVERT: A 730 THR cc_start: 0.8750 (m) cc_final: 0.8368 (p) REVERT: A 736 ASN cc_start: 0.8684 (m110) cc_final: 0.7829 (m-40) REVERT: A 850 ILE cc_start: 0.7974 (tt) cc_final: 0.7671 (tt) REVERT: B 95 GLU cc_start: 0.6991 (tp30) cc_final: 0.6478 (tp30) REVERT: B 295 GLN cc_start: 0.7772 (mm110) cc_final: 0.7141 (mm-40) REVERT: B 552 TRP cc_start: 0.7531 (OUTLIER) cc_final: 0.6149 (t-100) REVERT: B 563 HIS cc_start: 0.8767 (OUTLIER) cc_final: 0.7847 (m90) REVERT: B 652 MET cc_start: 0.6889 (mmm) cc_final: 0.6593 (mmm) REVERT: B 730 THR cc_start: 0.8853 (m) cc_final: 0.8560 (p) REVERT: B 736 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.7903 (m-40) REVERT: B 790 LYS cc_start: 0.7564 (mmtt) cc_final: 0.7167 (mptt) REVERT: B 850 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7592 (tt) outliers start: 33 outliers final: 26 residues processed: 155 average time/residue: 0.0810 time to fit residues: 19.1454 Evaluate side-chains 165 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 510 ASN Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 552 TRP Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 712 PHE Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 792 ASN Chi-restraints excluded: chain B residue 797 ARG Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 0.0040 chunk 102 optimal weight: 0.2980 chunk 110 optimal weight: 0.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 GLN B 510 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.143578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.112507 restraints weight = 15271.709| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.23 r_work: 0.3042 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13312 Z= 0.116 Angle : 0.477 8.277 18082 Z= 0.250 Chirality : 0.037 0.128 1984 Planarity : 0.004 0.029 2282 Dihedral : 4.177 49.106 1768 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.60 % Allowed : 13.22 % Favored : 84.18 % 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: 2.04 (0.22), residues: 1600 helix: 2.70 (0.17), residues: 980 sheet: -0.30 (0.41), residues: 174 loop : -1.13 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 164 TYR 0.013 0.001 TYR A 732 PHE 0.014 0.001 PHE B 601 TRP 0.005 0.001 TRP B 202 HIS 0.003 0.001 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (13312) covalent geometry : angle 0.47718 / 0.25 (18082) hydrogen bonds : bond 0.04989 / 3.41 ( 840) hydrogen bonds : angle 4.40150 / 3.26 ( 2472) =============================================================================== Job complete usr+sys time: 2824.58 seconds wall clock time: 49 minutes 0.33 seconds (2940.33 seconds total)