Starting phenix.real_space_refine on Wed Mar 4 09:54:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x06_32918/03_2026/7x06_32918.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x06_32918/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7x06_32918/03_2026/7x06_32918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x06_32918/03_2026/7x06_32918.map" model { file = "/net/cci-nas-00/data/ceres_data/7x06_32918/03_2026/7x06_32918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x06_32918/03_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-5986/lib/python3.9/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: 5.68, per 1000 atoms: 0.44 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: 0.85 Conformation dependent library (CDL) restraints added in 616.6 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: 0.37 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: 2.25 Time building geometry restraints manager: 1.19 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 - 17.04: 7361 17.04 - 34.08: 383 34.08 - 51.12: 54 51.12 - 68.15: 12 68.15 - 85.19: 8 Dihedral angle restraints: 7818 sinusoidal: 3108 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 7815 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.060 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 : 10.797 85.192 4794 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 covalent geometry : bond 0.00299 (13312) covalent geometry : angle 0.50784 (18082) hydrogen bonds : bond 0.11361 ( 840) hydrogen bonds : angle 5.13100 ( 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 : 0.448 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: 0.1158 time to fit residues: 36.6118 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 : 0.355 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.133215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.101224 restraints weight = 15501.154| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.28 r_work: 0.3033 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13312 Z= 0.216 Angle : 0.574 9.472 18082 Z= 0.303 Chirality : 0.041 0.141 1984 Planarity : 0.004 0.032 2282 Dihedral : 6.039 60.289 1834 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.73 % Allowed : 9.18 % 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: 1.63 (0.21), residues: 1600 helix: 2.32 (0.16), residues: 982 sheet: -0.36 (0.40), residues: 172 loop : -1.20 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 567 TYR 0.018 0.002 TYR A 492 PHE 0.017 0.002 PHE A 545 TRP 0.008 0.001 TRP A 804 HIS 0.004 0.001 HIS A 394 Details of bonding type rmsd covalent geometry : bond 0.00514 (13312) covalent geometry : angle 0.57396 (18082) hydrogen bonds : bond 0.06631 ( 840) hydrogen bonds : angle 4.77188 ( 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 180 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.2260 (mmm) cc_final: 0.1929 (mmp) REVERT: A 95 GLU cc_start: 0.7129 (tp30) cc_final: 0.6638 (tp30) REVERT: A 115 ASP cc_start: 0.7540 (m-30) cc_final: 0.6994 (t0) REVERT: A 244 GLN cc_start: 0.7670 (tp40) cc_final: 0.7395 (pm20) REVERT: A 299 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7801 (mmtm) REVERT: A 552 TRP cc_start: 0.7812 (OUTLIER) cc_final: 0.6391 (t-100) REVERT: A 730 THR cc_start: 0.8938 (m) cc_final: 0.8543 (p) REVERT: A 736 ASN cc_start: 0.8596 (m110) cc_final: 0.7873 (m-40) REVERT: A 850 ILE cc_start: 0.8153 (tt) cc_final: 0.7821 (tt) REVERT: B 71 MET cc_start: 0.4989 (mtt) cc_final: 0.4717 (ttm) REVERT: B 75 MET cc_start: 0.2749 (mmm) cc_final: 0.2332 (mmt) REVERT: B 244 GLN cc_start: 0.7631 (tp40) cc_final: 0.7391 (pm20) REVERT: B 475 GLN cc_start: 0.8073 (tt0) cc_final: 0.7870 (tt0) REVERT: B 552 TRP cc_start: 0.7799 (OUTLIER) cc_final: 0.6353 (t-100) REVERT: B 652 MET cc_start: 0.7214 (mmm) cc_final: 0.6930 (mmm) REVERT: B 730 THR cc_start: 0.9038 (m) cc_final: 0.8785 (p) REVERT: B 736 ASN cc_start: 0.8516 (m110) cc_final: 0.7614 (m-40) REVERT: B 790 LYS cc_start: 0.7825 (mmtt) cc_final: 0.7428 (mptt) REVERT: B 850 ILE cc_start: 0.8180 (tt) cc_final: 0.7849 (tt) outliers start: 24 outliers final: 17 residues processed: 169 average time/residue: 0.0959 time to fit residues: 24.8509 Evaluate side-chains 160 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 852 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 295 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.133321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.101426 restraints weight = 15710.328| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.27 r_work: 0.3118 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13312 Z= 0.165 Angle : 0.517 7.754 18082 Z= 0.275 Chirality : 0.039 0.132 1984 Planarity : 0.004 0.032 2282 Dihedral : 5.386 49.047 1832 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.38 % Allowed : 10.40 % Favored : 87.21 % 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: 1.63 (0.22), residues: 1600 helix: 2.31 (0.16), residues: 988 sheet: -0.79 (0.41), residues: 160 loop : -1.02 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 164 TYR 0.020 0.001 TYR B 732 PHE 0.014 0.001 PHE B 545 TRP 0.006 0.001 TRP A 804 HIS 0.003 0.001 HIS B 394 Details of bonding type rmsd covalent geometry : bond 0.00379 (13312) covalent geometry : angle 0.51747 (18082) hydrogen bonds : bond 0.06097 ( 840) hydrogen bonds : angle 4.64351 ( 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 178 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.5072 (OUTLIER) cc_final: 0.4694 (mtt) REVERT: A 75 MET cc_start: 0.2424 (mmm) cc_final: 0.2074 (mmp) REVERT: A 95 GLU cc_start: 0.7138 (tp30) cc_final: 0.6598 (tp30) REVERT: A 115 ASP cc_start: 0.7552 (m-30) cc_final: 0.7039 (t0) REVERT: A 244 GLN cc_start: 0.7615 (tp40) cc_final: 0.7395 (pm20) REVERT: A 299 LYS cc_start: 0.7918 (mmtt) cc_final: 0.7696 (mmtm) REVERT: A 552 TRP cc_start: 0.7846 (OUTLIER) cc_final: 0.6451 (t-100) REVERT: A 652 MET cc_start: 0.6998 (mmm) cc_final: 0.6767 (mmm) REVERT: A 730 THR cc_start: 0.8950 (m) cc_final: 0.8596 (p) REVERT: A 736 ASN cc_start: 0.8536 (m110) cc_final: 0.7818 (m-40) REVERT: A 850 ILE cc_start: 0.8161 (tt) cc_final: 0.7818 (tt) REVERT: B 71 MET cc_start: 0.5065 (mtt) cc_final: 0.4852 (ttm) REVERT: B 75 MET cc_start: 0.2819 (mmm) cc_final: 0.2369 (mmp) REVERT: B 244 GLN cc_start: 0.7606 (tp40) cc_final: 0.7405 (pm20) REVERT: B 552 TRP cc_start: 0.7785 (OUTLIER) cc_final: 0.6343 (t-100) REVERT: B 652 MET cc_start: 0.7237 (mmm) cc_final: 0.6947 (mmm) REVERT: B 730 THR cc_start: 0.8957 (m) cc_final: 0.8632 (p) REVERT: B 736 ASN cc_start: 0.8597 (m110) cc_final: 0.7687 (m-40) REVERT: B 790 LYS cc_start: 0.7842 (mmtt) cc_final: 0.7440 (mptt) REVERT: B 850 ILE cc_start: 0.8169 (tt) cc_final: 0.7839 (tt) outliers start: 33 outliers final: 24 residues processed: 169 average time/residue: 0.0957 time to fit residues: 24.5482 Evaluate side-chains 165 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 413 THR 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 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 327 HIS Chi-restraints excluded: chain B residue 333 LEU 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 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 693 LEU Chi-restraints excluded: chain B residue 797 ARG 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: 1.9990 chunk 79 optimal weight: 0.0980 chunk 23 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 156 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3532 r_free = 0.3532 target = 0.133669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.101312 restraints weight = 15574.742| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.35 r_work: 0.3071 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1670 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= 0.140 Angle : 0.495 7.447 18082 Z= 0.262 Chirality : 0.038 0.130 1984 Planarity : 0.004 0.031 2282 Dihedral : 5.035 49.032 1832 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.31 % Allowed : 11.42 % 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: 1.80 (0.22), residues: 1600 helix: 2.43 (0.16), residues: 988 sheet: -0.38 (0.40), residues: 172 loop : -1.09 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 164 TYR 0.021 0.001 TYR B 732 PHE 0.014 0.001 PHE A 601 TRP 0.005 0.001 TRP B 511 HIS 0.003 0.001 HIS B 709 Details of bonding type rmsd covalent geometry : bond 0.00308 (13312) covalent geometry : angle 0.49454 (18082) hydrogen bonds : bond 0.05693 ( 840) hydrogen bonds : angle 4.55364 ( 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 170 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.2461 (mmm) cc_final: 0.2098 (mmp) REVERT: A 95 GLU cc_start: 0.6948 (tp30) cc_final: 0.6399 (tp30) REVERT: A 115 ASP cc_start: 0.7403 (m-30) cc_final: 0.6903 (t0) REVERT: A 299 LYS cc_start: 0.7888 (mmtt) cc_final: 0.7647 (mmtm) REVERT: A 552 TRP cc_start: 0.7675 (OUTLIER) cc_final: 0.6256 (t-100) REVERT: A 730 THR cc_start: 0.8843 (m) cc_final: 0.8464 (p) REVERT: A 736 ASN cc_start: 0.8571 (m110) cc_final: 0.7853 (m-40) REVERT: A 850 ILE cc_start: 0.8058 (tt) cc_final: 0.7755 (tt) REVERT: B 95 GLU cc_start: 0.6744 (tp30) cc_final: 0.6296 (tp30) REVERT: B 552 TRP cc_start: 0.7579 (OUTLIER) cc_final: 0.6122 (t-100) REVERT: B 652 MET cc_start: 0.6941 (mmm) cc_final: 0.6707 (mmm) REVERT: B 730 THR cc_start: 0.8846 (m) cc_final: 0.8485 (p) REVERT: B 736 ASN cc_start: 0.8646 (m110) cc_final: 0.7875 (m-40) REVERT: B 790 LYS cc_start: 0.7713 (mmtt) cc_final: 0.7311 (mptt) REVERT: B 850 ILE cc_start: 0.8050 (tt) cc_final: 0.7754 (tt) outliers start: 32 outliers final: 22 residues processed: 158 average time/residue: 0.0999 time to fit residues: 23.9678 Evaluate side-chains 157 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 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 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 852 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 343 LEU 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 797 ARG 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: 1.9990 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 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: 2.9990 chunk 9 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 367 ASN ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 GLN B 367 ASN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.128882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.097100 restraints weight = 15785.224| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.24 r_work: 0.3029 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 13312 Z= 0.239 Angle : 0.584 8.586 18082 Z= 0.311 Chirality : 0.042 0.147 1984 Planarity : 0.004 0.036 2282 Dihedral : 5.248 49.455 1832 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.88 % Favored : 94.00 % Rotamer: Outliers : 3.40 % Allowed : 11.34 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.22), residues: 1600 helix: 2.13 (0.16), residues: 986 sheet: -0.57 (0.40), residues: 176 loop : -1.18 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 164 TYR 0.018 0.002 TYR B 473 PHE 0.019 0.002 PHE B 545 TRP 0.008 0.001 TRP A 511 HIS 0.005 0.001 HIS A 709 Details of bonding type rmsd covalent geometry : bond 0.00574 (13312) covalent geometry : angle 0.58404 (18082) hydrogen bonds : bond 0.07138 ( 840) hydrogen bonds : angle 4.74452 ( 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 186 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 139 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7185 (tp30) cc_final: 0.6601 (tp30) REVERT: A 115 ASP cc_start: 0.7580 (m-30) cc_final: 0.7130 (t0) REVERT: A 244 GLN cc_start: 0.7807 (tp40) cc_final: 0.7444 (pm20) REVERT: A 299 LYS cc_start: 0.8057 (mmtt) cc_final: 0.7810 (mmtm) REVERT: A 552 TRP cc_start: 0.7945 (OUTLIER) cc_final: 0.6640 (t-100) REVERT: A 730 THR cc_start: 0.9040 (m) cc_final: 0.8717 (p) REVERT: A 736 ASN cc_start: 0.8724 (m110) cc_final: 0.7993 (m-40) REVERT: B 95 GLU cc_start: 0.7108 (tp30) cc_final: 0.6610 (tp30) REVERT: B 552 TRP cc_start: 0.7885 (OUTLIER) cc_final: 0.6508 (t-100) REVERT: B 652 MET cc_start: 0.7103 (mmm) cc_final: 0.6848 (mmm) REVERT: B 730 THR cc_start: 0.9031 (m) cc_final: 0.8722 (p) REVERT: B 736 ASN cc_start: 0.8731 (m110) cc_final: 0.7975 (m-40) REVERT: B 790 LYS cc_start: 0.7842 (mmtt) cc_final: 0.7446 (mptt) outliers start: 47 outliers final: 32 residues processed: 173 average time/residue: 0.0953 time to fit residues: 25.1810 Evaluate side-chains 169 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 76 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 57 optimal weight: 0.0970 chunk 88 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN B 295 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.140217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.109117 restraints weight = 15293.631| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.21 r_work: 0.2998 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1972 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= 0.136 Angle : 0.497 7.683 18082 Z= 0.264 Chirality : 0.038 0.131 1984 Planarity : 0.004 0.031 2282 Dihedral : 5.129 52.181 1832 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.75 % Allowed : 12.36 % Favored : 84.90 % 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: 1.69 (0.22), residues: 1600 helix: 2.36 (0.16), residues: 988 sheet: -0.53 (0.40), residues: 176 loop : -1.14 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 164 TYR 0.014 0.001 TYR A 732 PHE 0.014 0.001 PHE A 545 TRP 0.005 0.001 TRP B 202 HIS 0.005 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00294 (13312) covalent geometry : angle 0.49725 (18082) hydrogen bonds : bond 0.05755 ( 840) hydrogen bonds : angle 4.57435 ( 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 181 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7030 (tp30) cc_final: 0.6451 (tp30) REVERT: A 115 ASP cc_start: 0.7429 (m-30) cc_final: 0.6849 (t0) REVERT: A 244 GLN cc_start: 0.7422 (tp40) cc_final: 0.7165 (pm20) REVERT: A 299 LYS cc_start: 0.7676 (mmtt) cc_final: 0.7447 (mmtm) REVERT: A 552 TRP cc_start: 0.7706 (OUTLIER) cc_final: 0.6385 (t-100) REVERT: A 730 THR cc_start: 0.8771 (m) cc_final: 0.8398 (p) REVERT: A 736 ASN cc_start: 0.8649 (m110) cc_final: 0.7817 (m-40) REVERT: B 95 GLU cc_start: 0.6965 (tp30) cc_final: 0.6458 (tp30) REVERT: B 295 GLN cc_start: 0.7828 (mm110) cc_final: 0.7190 (mm-40) REVERT: B 325 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8166 (mp10) REVERT: B 552 TRP cc_start: 0.7628 (OUTLIER) cc_final: 0.6248 (t-100) REVERT: B 652 MET cc_start: 0.6727 (mmm) cc_final: 0.6465 (mmm) REVERT: B 730 THR cc_start: 0.8786 (m) cc_final: 0.8417 (p) REVERT: B 736 ASN cc_start: 0.8643 (m110) cc_final: 0.7838 (m-40) REVERT: B 790 LYS cc_start: 0.7615 (mmtt) cc_final: 0.7215 (mptt) outliers start: 38 outliers final: 29 residues processed: 169 average time/residue: 0.0942 time to fit residues: 24.2611 Evaluate side-chains 167 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU 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 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 167 GLU Chi-restraints excluded: chain B residue 327 HIS 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 792 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 109 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 82 optimal weight: 0.0060 chunk 112 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.144086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.113540 restraints weight = 15218.706| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.15 r_work: 0.3022 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1994 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= 0.123 Angle : 0.483 7.296 18082 Z= 0.257 Chirality : 0.038 0.128 1984 Planarity : 0.004 0.030 2282 Dihedral : 5.076 56.358 1832 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.38 % Allowed : 13.29 % Favored : 84.32 % 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: 1.78 (0.22), residues: 1600 helix: 2.46 (0.17), residues: 988 sheet: -0.45 (0.41), residues: 174 loop : -1.20 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 164 TYR 0.013 0.001 TYR A 732 PHE 0.013 0.001 PHE A 601 TRP 0.006 0.001 TRP B 202 HIS 0.004 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00258 (13312) covalent geometry : angle 0.48341 (18082) hydrogen bonds : bond 0.05398 ( 840) hydrogen bonds : angle 4.49883 ( 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 169 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.3050 (mmp) cc_final: 0.2118 (mmm) REVERT: A 95 GLU cc_start: 0.7008 (tp30) cc_final: 0.6485 (tp30) REVERT: A 115 ASP cc_start: 0.7396 (m-30) cc_final: 0.6831 (t0) REVERT: A 299 LYS cc_start: 0.7664 (mmtt) cc_final: 0.7431 (mmtm) REVERT: A 325 GLN cc_start: 0.8427 (mm-40) cc_final: 0.8160 (mp10) REVERT: A 552 TRP cc_start: 0.7606 (OUTLIER) cc_final: 0.6305 (t-100) REVERT: A 730 THR cc_start: 0.8738 (m) cc_final: 0.8369 (p) REVERT: A 736 ASN cc_start: 0.8685 (m110) cc_final: 0.7829 (m-40) REVERT: B 95 GLU cc_start: 0.6928 (tp30) cc_final: 0.6409 (tp30) REVERT: B 295 GLN cc_start: 0.7789 (mm110) cc_final: 0.7171 (mm-40) REVERT: B 325 GLN cc_start: 0.8462 (mm-40) cc_final: 0.8176 (mp10) REVERT: B 552 TRP cc_start: 0.7499 (OUTLIER) cc_final: 0.6109 (t-100) REVERT: B 652 MET cc_start: 0.6679 (mmm) cc_final: 0.6425 (mmm) REVERT: B 730 THR cc_start: 0.8753 (m) cc_final: 0.8382 (p) REVERT: B 736 ASN cc_start: 0.8763 (m110) cc_final: 0.7914 (m-40) REVERT: B 790 LYS cc_start: 0.7597 (mmtt) cc_final: 0.7189 (mptt) outliers start: 33 outliers final: 27 residues processed: 158 average time/residue: 0.0965 time to fit residues: 23.6592 Evaluate side-chains 162 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 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 167 GLU Chi-restraints excluded: chain B residue 327 HIS 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 712 PHE 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: 1.9990 chunk 157 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 64 optimal weight: 0.0010 chunk 106 optimal weight: 1.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.139351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.108258 restraints weight = 15356.723| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.21 r_work: 0.2983 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13312 Z= 0.166 Angle : 0.516 7.493 18082 Z= 0.274 Chirality : 0.039 0.138 1984 Planarity : 0.004 0.030 2282 Dihedral : 5.174 59.164 1832 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.03 % Allowed : 12.86 % 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: 1.68 (0.22), residues: 1600 helix: 2.38 (0.16), residues: 988 sheet: -0.55 (0.40), residues: 176 loop : -1.21 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 797 TYR 0.013 0.001 TYR B 473 PHE 0.014 0.001 PHE B 545 TRP 0.006 0.001 TRP B 511 HIS 0.005 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00384 (13312) covalent geometry : angle 0.51600 (18082) hydrogen bonds : bond 0.06006 ( 840) hydrogen bonds : angle 4.55538 ( 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 182 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7149 (tp30) cc_final: 0.6591 (tp30) REVERT: A 115 ASP cc_start: 0.7432 (m-30) cc_final: 0.6942 (t0) REVERT: A 244 GLN cc_start: 0.7491 (tp40) cc_final: 0.7217 (pm20) REVERT: A 299 LYS cc_start: 0.7707 (mmtt) cc_final: 0.7484 (mmtm) REVERT: A 552 TRP cc_start: 0.7781 (OUTLIER) cc_final: 0.6490 (t-100) REVERT: A 730 THR cc_start: 0.8785 (m) cc_final: 0.8414 (p) REVERT: A 736 ASN cc_start: 0.8719 (m110) cc_final: 0.7890 (m-40) REVERT: B 95 GLU cc_start: 0.6992 (tp30) cc_final: 0.6452 (tp30) REVERT: B 295 GLN cc_start: 0.7764 (mm110) cc_final: 0.7126 (mm-40) REVERT: B 325 GLN cc_start: 0.8539 (mm-40) cc_final: 0.8240 (mp10) REVERT: B 510 ASN cc_start: 0.8982 (OUTLIER) cc_final: 0.8780 (p0) REVERT: B 552 TRP cc_start: 0.7676 (OUTLIER) cc_final: 0.6309 (t-100) REVERT: B 563 HIS cc_start: 0.8836 (OUTLIER) cc_final: 0.7943 (m90) REVERT: B 652 MET cc_start: 0.6765 (mmm) cc_final: 0.6508 (mmm) REVERT: B 730 THR cc_start: 0.8799 (m) cc_final: 0.8425 (p) REVERT: B 736 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8003 (m-40) REVERT: B 790 LYS cc_start: 0.7626 (mmtt) cc_final: 0.7220 (mptt) outliers start: 42 outliers final: 35 residues processed: 166 average time/residue: 0.0986 time to fit residues: 25.0841 Evaluate side-chains 178 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 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 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 A residue 852 THR 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 327 HIS 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 Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 78 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 82 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.143530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.113029 restraints weight = 15230.051| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.14 r_work: 0.3052 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13312 Z= 0.135 Angle : 0.491 7.269 18082 Z= 0.261 Chirality : 0.038 0.130 1984 Planarity : 0.004 0.030 2282 Dihedral : 5.124 58.173 1832 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.96 % Allowed : 13.15 % Favored : 83.89 % 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: 1.78 (0.22), residues: 1600 helix: 2.47 (0.16), residues: 988 sheet: -0.52 (0.41), residues: 176 loop : -1.17 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 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 0.005 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00294 (13312) covalent geometry : angle 0.49132 (18082) hydrogen bonds : bond 0.05517 ( 840) hydrogen bonds : angle 4.50402 ( 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 179 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.3118 (mmp) cc_final: 0.2190 (mmm) REVERT: A 95 GLU cc_start: 0.7174 (tp30) cc_final: 0.6632 (tp30) REVERT: A 115 ASP cc_start: 0.7447 (m-30) cc_final: 0.7019 (t0) REVERT: A 244 GLN cc_start: 0.7533 (tp40) cc_final: 0.7323 (pm20) REVERT: A 299 LYS cc_start: 0.7880 (mmtt) cc_final: 0.7663 (mmtm) REVERT: A 552 TRP cc_start: 0.7837 (OUTLIER) cc_final: 0.6534 (t-100) REVERT: A 730 THR cc_start: 0.8905 (m) cc_final: 0.8535 (p) REVERT: A 736 ASN cc_start: 0.8679 (m110) cc_final: 0.7904 (m-40) REVERT: B 95 GLU cc_start: 0.7052 (tp30) cc_final: 0.6527 (tp30) REVERT: B 295 GLN cc_start: 0.7826 (mm110) cc_final: 0.7239 (mm-40) REVERT: B 325 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8341 (mp10) REVERT: B 510 ASN cc_start: 0.9088 (OUTLIER) cc_final: 0.8885 (p0) REVERT: B 552 TRP cc_start: 0.7775 (OUTLIER) cc_final: 0.6398 (t-100) REVERT: B 563 HIS cc_start: 0.8860 (OUTLIER) cc_final: 0.7993 (m90) REVERT: B 652 MET cc_start: 0.6878 (mmm) cc_final: 0.6649 (mmm) REVERT: B 730 THR cc_start: 0.8909 (m) cc_final: 0.8543 (p) REVERT: B 736 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8010 (m-40) REVERT: B 790 LYS cc_start: 0.7723 (mmtt) cc_final: 0.7324 (mptt) outliers start: 41 outliers final: 32 residues processed: 164 average time/residue: 0.0987 time to fit residues: 24.7868 Evaluate side-chains 173 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 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 280 VAL Chi-restraints excluded: chain B residue 327 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 115 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 123 optimal weight: 0.2980 chunk 118 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.144223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.113800 restraints weight = 15237.741| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.15 r_work: 0.3076 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13312 Z= 0.127 Angle : 0.486 7.239 18082 Z= 0.258 Chirality : 0.038 0.130 1984 Planarity : 0.004 0.030 2282 Dihedral : 5.052 55.842 1832 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.11 % Allowed : 13.15 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.22), residues: 1600 helix: 2.54 (0.17), residues: 986 sheet: -0.49 (0.41), residues: 176 loop : -1.13 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 797 TYR 0.012 0.001 TYR B 732 PHE 0.013 0.001 PHE A 601 TRP 0.007 0.001 TRP A 511 HIS 0.004 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00271 (13312) covalent geometry : angle 0.48634 (18082) hydrogen bonds : bond 0.05325 ( 840) hydrogen bonds : angle 4.46832 ( 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 183 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 140 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7169 (tp30) cc_final: 0.6839 (tp30) REVERT: A 115 ASP cc_start: 0.7443 (m-30) cc_final: 0.6940 (t0) REVERT: A 299 LYS cc_start: 0.7823 (mmtt) cc_final: 0.7600 (mmtm) REVERT: A 552 TRP cc_start: 0.7706 (OUTLIER) cc_final: 0.6422 (t-100) REVERT: A 563 HIS cc_start: 0.8838 (OUTLIER) cc_final: 0.7948 (m90) REVERT: A 730 THR cc_start: 0.8857 (m) cc_final: 0.8487 (p) REVERT: A 736 ASN cc_start: 0.8647 (m110) cc_final: 0.7866 (m-40) REVERT: B 95 GLU cc_start: 0.7054 (tp30) cc_final: 0.6746 (tp30) REVERT: B 295 GLN cc_start: 0.7808 (mm110) cc_final: 0.7210 (mm-40) REVERT: B 325 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8313 (mp10) REVERT: B 510 ASN cc_start: 0.9070 (OUTLIER) cc_final: 0.8865 (p0) REVERT: B 552 TRP cc_start: 0.7662 (OUTLIER) cc_final: 0.6309 (t-100) REVERT: B 563 HIS cc_start: 0.8826 (OUTLIER) cc_final: 0.7939 (m90) REVERT: B 652 MET cc_start: 0.6817 (mmm) cc_final: 0.6589 (mmm) REVERT: B 730 THR cc_start: 0.8859 (m) cc_final: 0.8492 (p) REVERT: B 736 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.7953 (m-40) REVERT: B 790 LYS cc_start: 0.7674 (mmtt) cc_final: 0.7277 (mptt) outliers start: 43 outliers final: 33 residues processed: 167 average time/residue: 0.0960 time to fit residues: 24.5522 Evaluate side-chains 173 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 563 HIS Chi-restraints excluded: chain A residue 564 THR 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 327 HIS 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 Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 102 optimal weight: 0.0970 chunk 110 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.143123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.112686 restraints weight = 15205.473| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.14 r_work: 0.3027 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13312 Z= 0.151 Angle : 0.507 7.346 18082 Z= 0.269 Chirality : 0.039 0.135 1984 Planarity : 0.004 0.030 2282 Dihedral : 5.083 54.987 1832 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.25 % Allowed : 12.72 % Favored : 84.03 % 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: 1.78 (0.22), residues: 1600 helix: 2.46 (0.16), residues: 988 sheet: -0.50 (0.41), residues: 176 loop : -1.17 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 164 TYR 0.012 0.001 TYR B 732 PHE 0.014 0.001 PHE A 601 TRP 0.006 0.001 TRP A 511 HIS 0.005 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00341 (13312) covalent geometry : angle 0.50694 (18082) hydrogen bonds : bond 0.05639 ( 840) hydrogen bonds : angle 4.49727 ( 2472) =============================================================================== Job complete usr+sys time: 3135.48 seconds wall clock time: 54 minutes 20.00 seconds (3260.00 seconds total)