Starting phenix.real_space_refine on Wed Jul 30 19:23:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x06_32918/07_2025/7x06_32918.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x06_32918/07_2025/7x06_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_32918/07_2025/7x06_32918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x06_32918/07_2025/7x06_32918.map" model { file = "/net/cci-nas-00/data/ceres_data/7x06_32918/07_2025/7x06_32918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x06_32918/07_2025/7x06_32918.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 14.59, per 1000 atoms: 1.13 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: 3.38 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.52 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: 5.16 Time building geometry restraints manager: 3.96 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: 0.06 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 40.190 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.180 ------------------------------------------------------------------------------- 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 : 3.96 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP A 804 HIS 0.003 0.001 HIS B 709 PHE 0.012 0.001 PHE B 545 TYR 0.013 0.001 TYR B 473 ARG 0.003 0.000 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.11361 ( 840) hydrogen bonds : angle 5.13100 ( 2472) covalent geometry : bond 0.00299 (13312) covalent geometry : angle 0.50784 (18082) *********************** 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 : 1.803 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: 0.7930 (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: 0.3164 time to fit residues: 100.7282 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 : 1.614 ------------------------------------------------------------------------------- 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 135 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 B 318 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.135760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.105053 restraints weight = 15419.111| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.13 r_work: 0.3022 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 13312 Z= 0.332 Angle : 0.689 10.533 18082 Z= 0.367 Chirality : 0.047 0.155 1984 Planarity : 0.005 0.049 2282 Dihedral : 6.450 62.794 1834 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.69 % Favored : 94.19 % Rotamer: Outliers : 1.95 % Allowed : 9.90 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.21), residues: 1600 helix: 1.85 (0.16), residues: 986 sheet: -0.51 (0.40), residues: 172 loop : -1.27 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 804 HIS 0.006 0.002 HIS B 709 PHE 0.021 0.002 PHE B 329 TYR 0.024 0.002 TYR A 492 ARG 0.006 0.001 ARG B 497 Details of bonding type rmsd hydrogen bonds : bond 0.08258 ( 840) hydrogen bonds : angle 5.01810 ( 2472) covalent geometry : bond 0.00814 (13312) covalent geometry : angle 0.68895 (18082) *********************** 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 185 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7203 (tp30) cc_final: 0.6735 (tp30) REVERT: A 241 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8270 (mm-30) REVERT: A 244 GLN cc_start: 0.8006 (tp40) cc_final: 0.7625 (pm20) REVERT: A 299 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7926 (mmtm) REVERT: A 552 TRP cc_start: 0.7861 (OUTLIER) cc_final: 0.6477 (t-100) REVERT: A 652 MET cc_start: 0.7055 (mmm) cc_final: 0.6785 (mmm) REVERT: A 657 TYR cc_start: 0.7190 (t80) cc_final: 0.6700 (m-80) REVERT: A 736 ASN cc_start: 0.8620 (m110) cc_final: 0.7909 (m-40) REVERT: A 850 ILE cc_start: 0.8241 (tt) cc_final: 0.7916 (tt) REVERT: B 71 MET cc_start: 0.5045 (mtt) cc_final: 0.4769 (ttm) REVERT: B 75 MET cc_start: 0.2604 (mmm) cc_final: 0.2183 (mmt) REVERT: B 244 GLN cc_start: 0.8000 (tp40) cc_final: 0.7613 (pm20) REVERT: B 552 TRP cc_start: 0.7878 (OUTLIER) cc_final: 0.6475 (t-100) REVERT: B 652 MET cc_start: 0.7242 (mmm) cc_final: 0.6896 (mmm) REVERT: B 671 SER cc_start: 0.8769 (t) cc_final: 0.8558 (p) REVERT: B 736 ASN cc_start: 0.8657 (m110) cc_final: 0.7745 (m-40) REVERT: B 790 LYS cc_start: 0.7805 (mmtt) cc_final: 0.7422 (mptt) REVERT: B 850 ILE cc_start: 0.8234 (tt) cc_final: 0.7907 (tt) outliers start: 27 outliers final: 21 residues processed: 175 average time/residue: 0.2298 time to fit residues: 60.4962 Evaluate side-chains 165 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 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 852 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 280 VAL 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 688 ILE Chi-restraints excluded: chain B residue 797 ARG Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 31 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.142721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.111965 restraints weight = 15275.799| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.14 r_work: 0.2994 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13312 Z= 0.150 Angle : 0.515 7.564 18082 Z= 0.274 Chirality : 0.039 0.135 1984 Planarity : 0.004 0.033 2282 Dihedral : 5.589 50.052 1832 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.31 % Allowed : 10.98 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.22), residues: 1600 helix: 2.29 (0.16), residues: 976 sheet: -0.53 (0.40), residues: 174 loop : -1.17 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 202 HIS 0.003 0.001 HIS B 327 PHE 0.014 0.001 PHE B 601 TYR 0.018 0.001 TYR B 732 ARG 0.005 0.000 ARG B 164 Details of bonding type rmsd hydrogen bonds : bond 0.06082 ( 840) hydrogen bonds : angle 4.68802 ( 2472) covalent geometry : bond 0.00333 (13312) covalent geometry : angle 0.51454 (18082) *********************** 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 173 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.5101 (OUTLIER) cc_final: 0.4616 (mtt) REVERT: A 75 MET cc_start: 0.2107 (mmm) cc_final: 0.1831 (mmp) REVERT: A 95 GLU cc_start: 0.6957 (tp30) cc_final: 0.6410 (tp30) REVERT: A 244 GLN cc_start: 0.7466 (tp40) cc_final: 0.7193 (pm20) REVERT: A 334 GLN cc_start: 0.9282 (OUTLIER) cc_final: 0.8928 (mt0) REVERT: A 382 ASP cc_start: 0.8807 (m-30) cc_final: 0.8540 (m-30) REVERT: A 552 TRP cc_start: 0.7636 (OUTLIER) cc_final: 0.6245 (t-100) REVERT: A 730 THR cc_start: 0.8718 (m) cc_final: 0.8314 (p) REVERT: A 736 ASN cc_start: 0.8495 (m110) cc_final: 0.7622 (m-40) REVERT: A 850 ILE cc_start: 0.7999 (tt) cc_final: 0.7678 (tt) REVERT: B 71 MET cc_start: 0.4855 (mtt) cc_final: 0.4579 (ttm) REVERT: B 75 MET cc_start: 0.2512 (mmm) cc_final: 0.2130 (mmp) REVERT: B 244 GLN cc_start: 0.7459 (tp40) cc_final: 0.7204 (pm20) REVERT: B 334 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8901 (mt0) REVERT: B 552 TRP cc_start: 0.7642 (OUTLIER) cc_final: 0.6245 (t-100) REVERT: B 652 MET cc_start: 0.6800 (mmm) cc_final: 0.6474 (mmm) REVERT: B 730 THR cc_start: 0.8745 (m) cc_final: 0.8400 (p) REVERT: B 736 ASN cc_start: 0.8529 (m110) cc_final: 0.7662 (m-40) REVERT: B 790 LYS cc_start: 0.7640 (mmtt) cc_final: 0.7231 (mptt) REVERT: B 850 ILE cc_start: 0.7983 (tt) cc_final: 0.7684 (tt) outliers start: 32 outliers final: 20 residues processed: 163 average time/residue: 0.3052 time to fit residues: 75.3550 Evaluate side-chains 160 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 413 THR 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 693 LEU 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 334 GLN Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 413 THR 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 16 optimal weight: 0.9980 chunk 148 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 57 optimal weight: 0.0020 chunk 126 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3553 r_free = 0.3553 target = 0.135354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.103495 restraints weight = 15402.851| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.30 r_work: 0.3108 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1786 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= 0.124 Angle : 0.479 7.069 18082 Z= 0.254 Chirality : 0.038 0.130 1984 Planarity : 0.004 0.031 2282 Dihedral : 4.957 49.314 1832 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.75 % Allowed : 11.63 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.22), residues: 1600 helix: 2.50 (0.17), residues: 986 sheet: -0.44 (0.41), residues: 172 loop : -1.10 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 202 HIS 0.003 0.001 HIS B 327 PHE 0.014 0.001 PHE A 601 TYR 0.018 0.001 TYR A 732 ARG 0.009 0.000 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.05378 ( 840) hydrogen bonds : angle 4.52442 ( 2472) covalent geometry : bond 0.00260 (13312) covalent geometry : angle 0.47877 (18082) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7085 (tp30) cc_final: 0.6533 (tp30) REVERT: A 115 ASP cc_start: 0.7743 (m-30) cc_final: 0.6983 (t0) REVERT: A 240 ASN cc_start: 0.7585 (t0) cc_final: 0.7334 (t0) REVERT: A 241 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7757 (mp0) REVERT: A 325 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8390 (mp10) REVERT: A 334 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8832 (mt0) REVERT: A 552 TRP cc_start: 0.7713 (OUTLIER) cc_final: 0.6355 (t-100) REVERT: A 730 THR cc_start: 0.8908 (m) cc_final: 0.8533 (p) REVERT: A 736 ASN cc_start: 0.8643 (m110) cc_final: 0.7904 (m-40) REVERT: A 850 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7798 (tt) REVERT: B 75 MET cc_start: 0.2817 (mmm) cc_final: 0.2359 (mmp) REVERT: B 91 ILE cc_start: 0.7126 (OUTLIER) cc_final: 0.6916 (tt) REVERT: B 95 GLU cc_start: 0.7030 (tp30) cc_final: 0.6815 (tp30) REVERT: B 334 GLN cc_start: 0.9257 (OUTLIER) cc_final: 0.8826 (mt0) REVERT: B 552 TRP cc_start: 0.7741 (OUTLIER) cc_final: 0.6331 (t-100) REVERT: B 652 MET cc_start: 0.6974 (mmm) cc_final: 0.6730 (mmm) REVERT: B 730 THR cc_start: 0.8899 (m) cc_final: 0.8535 (p) REVERT: B 736 ASN cc_start: 0.8607 (m110) cc_final: 0.7885 (m-40) REVERT: B 790 LYS cc_start: 0.7760 (mmtt) cc_final: 0.7350 (mptt) REVERT: B 850 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7818 (tt) outliers start: 38 outliers final: 22 residues processed: 163 average time/residue: 0.2322 time to fit residues: 57.3292 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 : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 334 GLN 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 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 850 ILE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 334 GLN 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 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 850 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 27 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN ** B 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.128336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.096915 restraints weight = 15759.872| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.23 r_work: 0.3092 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 13312 Z= 0.232 Angle : 0.573 8.463 18082 Z= 0.306 Chirality : 0.042 0.148 1984 Planarity : 0.004 0.037 2282 Dihedral : 5.217 49.595 1832 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.94 % Favored : 93.94 % Rotamer: Outliers : 2.82 % Allowed : 12.07 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.22), residues: 1600 helix: 2.15 (0.16), residues: 986 sheet: -0.64 (0.40), residues: 176 loop : -1.30 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 511 HIS 0.006 0.001 HIS B 709 PHE 0.019 0.002 PHE A 545 TYR 0.017 0.002 TYR B 473 ARG 0.009 0.001 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.07074 ( 840) hydrogen bonds : angle 4.73094 ( 2472) covalent geometry : bond 0.00559 (13312) covalent geometry : angle 0.57315 (18082) *********************** 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 177 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7174 (tp30) cc_final: 0.6589 (tp30) REVERT: A 115 ASP cc_start: 0.7772 (m-30) cc_final: 0.7109 (t0) REVERT: A 244 GLN cc_start: 0.7802 (tp40) cc_final: 0.7443 (pm20) REVERT: A 334 GLN cc_start: 0.9323 (OUTLIER) cc_final: 0.9053 (mt0) REVERT: A 552 TRP cc_start: 0.7939 (OUTLIER) cc_final: 0.6649 (t-100) REVERT: A 730 THR cc_start: 0.9028 (m) cc_final: 0.8701 (p) REVERT: A 736 ASN cc_start: 0.8724 (m110) cc_final: 0.8060 (m-40) REVERT: B 95 GLU cc_start: 0.7106 (tp30) cc_final: 0.6597 (tp30) REVERT: B 244 GLN cc_start: 0.7787 (tp40) cc_final: 0.7440 (pm20) REVERT: B 334 GLN cc_start: 0.9317 (OUTLIER) cc_final: 0.9053 (mt0) REVERT: B 552 TRP cc_start: 0.7879 (OUTLIER) cc_final: 0.6523 (t-100) REVERT: B 652 MET cc_start: 0.7048 (mmm) cc_final: 0.6792 (mmm) REVERT: B 730 THR cc_start: 0.9025 (m) cc_final: 0.8705 (p) REVERT: B 736 ASN cc_start: 0.8749 (m110) cc_final: 0.8012 (m-40) REVERT: B 790 LYS cc_start: 0.7803 (mmtt) cc_final: 0.7389 (mptt) outliers start: 39 outliers final: 31 residues processed: 166 average time/residue: 0.2461 time to fit residues: 63.2096 Evaluate side-chains 170 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 333 LEU Chi-restraints excluded: chain A residue 334 GLN 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 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 A residue 852 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 334 GLN 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 496 ASP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 552 TRP Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 797 ARG Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 850 ILE 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 25 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 295 GLN ** B 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.139289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.108708 restraints weight = 15537.431| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.14 r_work: 0.2974 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2069 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= 0.180 Angle : 0.528 7.719 18082 Z= 0.282 Chirality : 0.040 0.136 1984 Planarity : 0.004 0.032 2282 Dihedral : 5.198 50.168 1832 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.82 % Allowed : 12.93 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.22), residues: 1600 helix: 2.21 (0.16), residues: 986 sheet: -0.71 (0.40), residues: 176 loop : -1.33 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 511 HIS 0.003 0.001 HIS A 709 PHE 0.017 0.001 PHE B 545 TYR 0.013 0.001 TYR B 473 ARG 0.002 0.000 ARG A 797 Details of bonding type rmsd hydrogen bonds : bond 0.06377 ( 840) hydrogen bonds : angle 4.66165 ( 2472) covalent geometry : bond 0.00419 (13312) covalent geometry : angle 0.52818 (18082) *********************** 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: 39 poor density : 142 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7028 (tp30) cc_final: 0.6449 (tp30) REVERT: A 115 ASP cc_start: 0.7645 (m-30) cc_final: 0.6926 (t0) REVERT: A 244 GLN cc_start: 0.7566 (tp40) cc_final: 0.7214 (pm20) REVERT: A 552 TRP cc_start: 0.7749 (OUTLIER) cc_final: 0.6468 (t-100) REVERT: A 730 THR cc_start: 0.8801 (m) cc_final: 0.8422 (p) REVERT: A 736 ASN cc_start: 0.8691 (m110) cc_final: 0.7918 (m-40) REVERT: B 95 GLU cc_start: 0.6968 (tp30) cc_final: 0.6473 (tp30) REVERT: B 244 GLN cc_start: 0.7554 (tp40) cc_final: 0.7239 (pm20) REVERT: B 295 GLN cc_start: 0.7824 (mm110) cc_final: 0.7191 (mm-40) REVERT: B 334 GLN cc_start: 0.9276 (OUTLIER) cc_final: 0.9004 (mt0) REVERT: B 552 TRP cc_start: 0.7687 (OUTLIER) cc_final: 0.6346 (t-100) REVERT: B 652 MET cc_start: 0.6770 (mmm) cc_final: 0.6484 (mmm) REVERT: B 730 THR cc_start: 0.8815 (m) cc_final: 0.8468 (p) REVERT: B 736 ASN cc_start: 0.8727 (m110) cc_final: 0.7896 (m-40) REVERT: B 790 LYS cc_start: 0.7593 (mmtt) cc_final: 0.7200 (mptt) outliers start: 39 outliers final: 29 residues processed: 171 average time/residue: 0.2190 time to fit residues: 57.0625 Evaluate side-chains 169 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 204 THR Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 334 GLN 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 23 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 64 optimal weight: 0.0970 chunk 6 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.140081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.109550 restraints weight = 15347.545| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.14 r_work: 0.2989 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 13312 Z= 0.159 Angle : 0.514 7.476 18082 Z= 0.273 Chirality : 0.039 0.136 1984 Planarity : 0.004 0.031 2282 Dihedral : 5.198 55.898 1832 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.96 % Allowed : 13.22 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.22), residues: 1600 helix: 2.29 (0.16), residues: 988 sheet: -0.70 (0.40), residues: 176 loop : -1.28 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 202 HIS 0.003 0.001 HIS A 709 PHE 0.016 0.001 PHE A 545 TYR 0.013 0.001 TYR B 732 ARG 0.004 0.000 ARG B 164 Details of bonding type rmsd hydrogen bonds : bond 0.06055 ( 840) hydrogen bonds : angle 4.60501 ( 2472) covalent geometry : bond 0.00361 (13312) covalent geometry : angle 0.51403 (18082) *********************** 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 181 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 140 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7097 (tp30) cc_final: 0.6554 (tp30) REVERT: A 115 ASP cc_start: 0.7624 (m-30) cc_final: 0.6931 (t0) REVERT: A 244 GLN cc_start: 0.7523 (tp40) cc_final: 0.7242 (pm20) REVERT: A 334 GLN cc_start: 0.9306 (OUTLIER) cc_final: 0.8991 (mt0) REVERT: A 552 TRP cc_start: 0.7733 (OUTLIER) cc_final: 0.6449 (t-100) REVERT: A 730 THR cc_start: 0.8786 (m) cc_final: 0.8409 (p) REVERT: A 736 ASN cc_start: 0.8683 (m110) cc_final: 0.7871 (m-40) REVERT: B 95 GLU cc_start: 0.7022 (tp30) cc_final: 0.6505 (tp30) REVERT: B 244 GLN cc_start: 0.7513 (tp40) cc_final: 0.7237 (pm20) REVERT: B 295 GLN cc_start: 0.7759 (mm110) cc_final: 0.7126 (mm-40) REVERT: B 334 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.8968 (mt0) REVERT: B 552 TRP cc_start: 0.7706 (OUTLIER) cc_final: 0.6403 (t-100) REVERT: B 563 HIS cc_start: 0.8870 (OUTLIER) cc_final: 0.7996 (m90) REVERT: B 652 MET cc_start: 0.6759 (mmm) cc_final: 0.6480 (mmm) REVERT: B 730 THR cc_start: 0.8789 (m) cc_final: 0.8416 (p) REVERT: B 736 ASN cc_start: 0.8759 (m110) cc_final: 0.7976 (m-40) REVERT: B 790 LYS cc_start: 0.7577 (mmtt) cc_final: 0.7171 (mptt) outliers start: 41 outliers final: 35 residues processed: 172 average time/residue: 0.2205 time to fit residues: 58.0231 Evaluate side-chains 175 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 334 GLN 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 496 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 651 HIS 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 B residue 167 GLU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 334 GLN 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 496 ASP 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 564 THR 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 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 Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 112 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 139 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.130548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.098686 restraints weight = 15798.877| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.30 r_work: 0.3072 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2158 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= 0.180 Angle : 0.530 7.687 18082 Z= 0.282 Chirality : 0.040 0.139 1984 Planarity : 0.004 0.032 2282 Dihedral : 5.261 58.682 1832 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.68 % Allowed : 13.15 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.22), residues: 1600 helix: 2.24 (0.16), residues: 986 sheet: -0.69 (0.40), residues: 176 loop : -1.32 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 511 HIS 0.003 0.001 HIS A 709 PHE 0.016 0.001 PHE A 545 TYR 0.015 0.001 TYR A 732 ARG 0.002 0.000 ARG A 797 Details of bonding type rmsd hydrogen bonds : bond 0.06324 ( 840) hydrogen bonds : angle 4.63214 ( 2472) covalent geometry : bond 0.00419 (13312) covalent geometry : angle 0.53047 (18082) *********************** 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 190 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 139 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7255 (tp30) cc_final: 0.6750 (tp30) REVERT: A 115 ASP cc_start: 0.7718 (m-30) cc_final: 0.7088 (t0) REVERT: A 244 GLN cc_start: 0.7686 (tp40) cc_final: 0.7381 (pm20) REVERT: A 325 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8450 (mp10) REVERT: A 552 TRP cc_start: 0.7924 (OUTLIER) cc_final: 0.6682 (t-100) REVERT: A 563 HIS cc_start: 0.8929 (OUTLIER) cc_final: 0.8100 (m90) REVERT: A 730 THR cc_start: 0.8961 (m) cc_final: 0.8595 (p) REVERT: A 736 ASN cc_start: 0.8754 (m110) cc_final: 0.8080 (m-40) REVERT: B 95 GLU cc_start: 0.7136 (tp30) cc_final: 0.6625 (tp30) REVERT: B 244 GLN cc_start: 0.7686 (tp40) cc_final: 0.7394 (pm20) REVERT: B 295 GLN cc_start: 0.7890 (mm110) cc_final: 0.7293 (mm-40) REVERT: B 334 GLN cc_start: 0.9309 (OUTLIER) cc_final: 0.9036 (mt0) REVERT: B 552 TRP cc_start: 0.7889 (OUTLIER) cc_final: 0.6618 (t-100) REVERT: B 563 HIS cc_start: 0.8929 (OUTLIER) cc_final: 0.8103 (m90) REVERT: B 652 MET cc_start: 0.7013 (mmm) cc_final: 0.6755 (mmm) REVERT: B 730 THR cc_start: 0.8959 (m) cc_final: 0.8595 (p) REVERT: B 736 ASN cc_start: 0.8794 (m110) cc_final: 0.8077 (m-40) REVERT: B 790 LYS cc_start: 0.7706 (mmtt) cc_final: 0.7307 (mptt) outliers start: 51 outliers final: 38 residues processed: 176 average time/residue: 0.3086 time to fit residues: 85.0306 Evaluate side-chains 182 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 325 GLN 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 496 ASP 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 651 HIS 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 A residue 852 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 334 GLN 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 496 ASP 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 564 THR 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 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 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 3 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 28 optimal weight: 0.0970 chunk 112 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 125 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3654 r_free = 0.3654 target = 0.142920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.112421 restraints weight = 15181.970| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.14 r_work: 0.3026 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13312 Z= 0.119 Angle : 0.484 6.864 18082 Z= 0.257 Chirality : 0.037 0.128 1984 Planarity : 0.004 0.031 2282 Dihedral : 5.127 58.175 1832 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.67 % Allowed : 13.80 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.22), residues: 1600 helix: 2.49 (0.17), residues: 986 sheet: -0.61 (0.40), residues: 176 loop : -1.22 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 202 HIS 0.002 0.001 HIS A 709 PHE 0.013 0.001 PHE A 601 TYR 0.014 0.001 TYR A 732 ARG 0.005 0.000 ARG B 164 Details of bonding type rmsd hydrogen bonds : bond 0.05267 ( 840) hydrogen bonds : angle 4.50552 ( 2472) covalent geometry : bond 0.00240 (13312) covalent geometry : angle 0.48437 (18082) *********************** 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 175 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7055 (tp30) cc_final: 0.6495 (tp30) REVERT: A 115 ASP cc_start: 0.7496 (m-30) cc_final: 0.6823 (t0) REVERT: A 244 GLN cc_start: 0.7406 (tp40) cc_final: 0.7177 (pm20) REVERT: A 325 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8186 (mp10) REVERT: A 552 TRP cc_start: 0.7612 (OUTLIER) cc_final: 0.6338 (t-100) REVERT: A 563 HIS cc_start: 0.8816 (OUTLIER) cc_final: 0.7909 (m90) REVERT: A 730 THR cc_start: 0.8755 (m) cc_final: 0.8371 (p) REVERT: A 736 ASN cc_start: 0.8674 (m110) cc_final: 0.7794 (m-40) REVERT: B 95 GLU cc_start: 0.6926 (tp30) cc_final: 0.6375 (tp30) REVERT: B 295 GLN cc_start: 0.7707 (mm110) cc_final: 0.7078 (mm-40) REVERT: B 334 GLN cc_start: 0.9254 (OUTLIER) cc_final: 0.8867 (mt0) REVERT: B 552 TRP cc_start: 0.7595 (OUTLIER) cc_final: 0.6295 (t-100) REVERT: B 563 HIS cc_start: 0.8827 (OUTLIER) cc_final: 0.7919 (m90) REVERT: B 652 MET cc_start: 0.6676 (mmm) cc_final: 0.6410 (mmm) REVERT: B 730 THR cc_start: 0.8742 (m) cc_final: 0.8361 (p) REVERT: B 736 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.7845 (m-40) REVERT: B 790 LYS cc_start: 0.7546 (mmtt) cc_final: 0.7152 (mptt) outliers start: 37 outliers final: 30 residues processed: 162 average time/residue: 0.2512 time to fit residues: 62.0402 Evaluate side-chains 174 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU 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 496 ASP 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 651 HIS 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 204 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 334 GLN 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 496 ASP 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 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 144 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.137698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.107186 restraints weight = 15425.844| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.13 r_work: 0.3070 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13312 Z= 0.224 Angle : 0.573 8.224 18082 Z= 0.305 Chirality : 0.041 0.148 1984 Planarity : 0.004 0.030 2282 Dihedral : 5.311 56.485 1832 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.56 % Favored : 93.38 % Rotamer: Outliers : 3.11 % Allowed : 13.73 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.22), residues: 1600 helix: 2.19 (0.16), residues: 988 sheet: -0.67 (0.40), residues: 176 loop : -1.32 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 511 HIS 0.004 0.001 HIS B 709 PHE 0.020 0.002 PHE A 545 TYR 0.015 0.002 TYR B 473 ARG 0.003 0.001 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.06894 ( 840) hydrogen bonds : angle 4.68323 ( 2472) covalent geometry : bond 0.00534 (13312) covalent geometry : angle 0.57262 (18082) ********************** 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 179 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7342 (tp30) cc_final: 0.6789 (tp30) REVERT: A 115 ASP cc_start: 0.7744 (m-30) cc_final: 0.7151 (t0) REVERT: A 244 GLN cc_start: 0.7791 (tp40) cc_final: 0.7437 (pm20) REVERT: A 325 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8480 (mp10) REVERT: A 552 TRP cc_start: 0.7998 (OUTLIER) cc_final: 0.6743 (t-100) REVERT: A 563 HIS cc_start: 0.8972 (OUTLIER) cc_final: 0.8219 (m90) REVERT: A 730 THR cc_start: 0.9024 (m) cc_final: 0.8708 (p) REVERT: A 736 ASN cc_start: 0.8818 (m110) cc_final: 0.8155 (m-40) REVERT: B 95 GLU cc_start: 0.7159 (tp30) cc_final: 0.6625 (tp30) REVERT: B 115 ASP cc_start: 0.6565 (t0) cc_final: 0.6345 (t0) REVERT: B 244 GLN cc_start: 0.7775 (tp40) cc_final: 0.7441 (pm20) REVERT: B 295 GLN cc_start: 0.7908 (mm110) cc_final: 0.7325 (mm-40) REVERT: B 552 TRP cc_start: 0.7972 (OUTLIER) cc_final: 0.6730 (t-100) REVERT: B 563 HIS cc_start: 0.8986 (OUTLIER) cc_final: 0.8181 (m90) REVERT: B 652 MET cc_start: 0.7005 (mmm) cc_final: 0.6674 (mmm) REVERT: B 730 THR cc_start: 0.9087 (m) cc_final: 0.8849 (p) REVERT: B 736 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8119 (m-40) REVERT: B 790 LYS cc_start: 0.7729 (mmtt) cc_final: 0.7334 (mptt) outliers start: 43 outliers final: 33 residues processed: 167 average time/residue: 0.2234 time to fit residues: 57.1636 Evaluate side-chains 175 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 325 GLN 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 496 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 651 HIS 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 127 MET Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 204 THR 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 413 THR 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 563 HIS 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 30 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 116 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.132644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.100692 restraints weight = 15654.681| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.30 r_work: 0.3120 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13312 Z= 0.136 Angle : 0.502 7.032 18082 Z= 0.266 Chirality : 0.038 0.131 1984 Planarity : 0.004 0.031 2282 Dihedral : 5.185 54.432 1832 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.60 % Allowed : 14.09 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.22), residues: 1600 helix: 2.38 (0.17), residues: 988 sheet: -0.66 (0.40), residues: 176 loop : -1.28 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 202 HIS 0.002 0.001 HIS B 709 PHE 0.014 0.001 PHE B 545 TYR 0.013 0.001 TYR A 732 ARG 0.002 0.000 ARG B 780 Details of bonding type rmsd hydrogen bonds : bond 0.05703 ( 840) hydrogen bonds : angle 4.55133 ( 2472) covalent geometry : bond 0.00292 (13312) covalent geometry : angle 0.50177 (18082) =============================================================================== Job complete usr+sys time: 7765.97 seconds wall clock time: 137 minutes 54.07 seconds (8274.07 seconds total)