Starting phenix.real_space_refine on Thu Jun 4 04:23:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rd8_53929/06_2026/9rd8_53929.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rd8_53929/06_2026/9rd8_53929.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rd8_53929/06_2026/9rd8_53929.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rd8_53929/06_2026/9rd8_53929.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rd8_53929/06_2026/9rd8_53929.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rd8_53929/06_2026/9rd8_53929.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.021 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 Zn 1 6.06 5 P 4 5.49 5 S 31 5.16 5 C 6646 2.51 5 N 1804 2.21 5 O 1843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10329 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6176 Classifications: {'peptide': 787} Link IDs: {'PTRANS': 35, 'TRANS': 751} Chain breaks: 3 Chain: "B" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3978 Classifications: {'peptide': 524} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 508} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 54 Unusual residues: {' ZN': 1, '6OU': 1, 'BCT': 1, 'CO2': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 121 Unusual residues: {'6OU': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'6OU:plan-1': 2} Unresolved non-hydrogen planarities: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2496 SG CYS A 351 42.577 59.792 34.694 1.00 14.34 S ATOM 3937 SG CYS A 539 45.083 60.072 38.067 1.00 15.86 S Time building chain proxies: 2.53, per 1000 atoms: 0.24 Number of scatterers: 10329 At special positions: 0 Unit cell: (83.22, 97.09, 124.83, 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) Zn 1 29.99 S 31 16.00 P 4 15.00 O 1843 8.00 N 1804 7.00 C 6646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 461.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 351 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 539 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 524 " 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2428 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 5 sheets defined 65.6% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 10 through 27 removed outlier: 3.597A pdb=" N ARG A 27 " --> pdb=" O LYS A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 37 removed outlier: 3.773A pdb=" N PHE A 37 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 47 removed outlier: 3.930A pdb=" N ILE A 47 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 69 through 78 removed outlier: 3.896A pdb=" N PHE A 73 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS A 76 " --> pdb=" O TRP A 72 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 95 Processing helix chain 'A' and resid 99 through 107 removed outlier: 3.674A pdb=" N LEU A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 148 Processing helix chain 'A' and resid 164 through 176 Processing helix chain 'A' and resid 177 through 183 removed outlier: 4.197A pdb=" N ALA A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'A' and resid 197 through 210 Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 215 through 226 Processing helix chain 'A' and resid 227 through 245 removed outlier: 3.539A pdb=" N ALA A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 269 removed outlier: 3.545A pdb=" N THR A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 305 through 327 removed outlier: 3.892A pdb=" N ILE A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG A 324 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE A 325 " --> pdb=" O PHE A 321 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 367 removed outlier: 4.152A pdb=" N PHE A 359 " --> pdb=" O ARG A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 435 removed outlier: 3.621A pdb=" N ALA A 416 " --> pdb=" O ASP A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 447 Processing helix chain 'A' and resid 449 through 459 removed outlier: 3.718A pdb=" N ARG A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 494 through 510 Processing helix chain 'A' and resid 533 through 537 Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 560 through 567 Processing helix chain 'A' and resid 603 through 626 Processing helix chain 'A' and resid 637 through 645 removed outlier: 4.090A pdb=" N GLN A 641 " --> pdb=" O ASP A 637 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG A 645 " --> pdb=" O GLN A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 673 removed outlier: 4.285A pdb=" N THR A 672 " --> pdb=" O PRO A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 691 Processing helix chain 'A' and resid 696 through 701 Processing helix chain 'A' and resid 702 through 721 removed outlier: 3.580A pdb=" N ILE A 706 " --> pdb=" O THR A 702 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 731 No H-bonds generated for 'chain 'A' and resid 729 through 731' Processing helix chain 'A' and resid 755 through 759 Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 790 through 799 Processing helix chain 'B' and resid 7 through 23 Proline residue: B 17 - end of helix removed outlier: 3.890A pdb=" N LEU B 20 " --> pdb=" O MET B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 63 Processing helix chain 'B' and resid 78 through 82 removed outlier: 3.601A pdb=" N LEU B 81 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 114 removed outlier: 4.197A pdb=" N GLN B 112 " --> pdb=" O ARG B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 140 Processing helix chain 'B' and resid 142 through 162 removed outlier: 3.503A pdb=" N SER B 162 " --> pdb=" O HIS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 200 removed outlier: 3.697A pdb=" N PHE B 180 " --> pdb=" O LYS B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 218 through 236 Processing helix chain 'B' and resid 242 through 247 removed outlier: 3.613A pdb=" N ILE B 246 " --> pdb=" O HIS B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 261 Processing helix chain 'B' and resid 265 through 274 Processing helix chain 'B' and resid 274 through 280 removed outlier: 3.519A pdb=" N ALA B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 304 removed outlier: 3.961A pdb=" N LEU B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 304 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 330 Processing helix chain 'B' and resid 332 through 353 removed outlier: 3.545A pdb=" N ALA B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 361 removed outlier: 4.094A pdb=" N ASP B 359 " --> pdb=" O GLY B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 395 removed outlier: 3.501A pdb=" N TRP B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.756A pdb=" N VAL B 408 " --> pdb=" O MET B 404 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N MET B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N HIS B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 457 removed outlier: 3.930A pdb=" N PHE B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 491 Processing helix chain 'B' and resid 492 through 497 removed outlier: 3.798A pdb=" N MET B 497 " --> pdb=" O GLY B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 511 Processing helix chain 'B' and resid 514 through 527 removed outlier: 3.915A pdb=" N TRP B 518 " --> pdb=" O TYR B 514 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 370 through 374 removed outlier: 6.299A pdb=" N VAL A 346 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ILE A 373 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ALA A 348 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL A 519 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ALA A 583 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU A 521 " --> pdb=" O ALA A 583 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N HIS A 585 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLY A 523 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA A 582 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 394 through 395 removed outlier: 6.150A pdb=" N ASP A 384 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N GLU A 409 " --> pdb=" O ASP A 384 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N CYS A 386 " --> pdb=" O GLU A 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 682 through 684 removed outlier: 6.775A pdb=" N ALA A 663 " --> pdb=" O PHE A 682 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N HIS A 684 " --> pdb=" O ALA A 663 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE A 665 " --> pdb=" O HIS A 684 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE A 664 " --> pdb=" O TYR A 775 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ILE A 804 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASP A 821 " --> pdb=" O HIS A 817 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 733 through 736 Processing sheet with id=AA5, first strand: chain 'B' and resid 68 through 70 611 hydrogen bonds defined for protein. 1788 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.63 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.29: 1655 1.29 - 1.42: 2723 1.42 - 1.55: 6108 1.55 - 1.68: 8 1.68 - 1.81: 55 Bond restraints: 10549 Sorted by residual: bond pdb=" N LEU B 75 " pdb=" CA LEU B 75 " ideal model delta sigma weight residual 1.455 1.482 -0.027 7.00e-03 2.04e+04 1.43e+01 bond pdb=" N ASP A 353 " pdb=" CA ASP A 353 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.32e-02 5.74e+03 7.89e+00 bond pdb=" N VAL A 109 " pdb=" CA VAL A 109 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.68e+00 bond pdb=" N ASN A 282 " pdb=" CA ASN A 282 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.89e+00 bond pdb=" C GLN A 332 " pdb=" N PRO A 333 " ideal model delta sigma weight residual 1.331 1.361 -0.030 1.20e-02 6.94e+03 6.25e+00 ... (remaining 10544 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 14104 2.20 - 4.40: 170 4.40 - 6.60: 27 6.60 - 8.80: 3 8.80 - 11.00: 3 Bond angle restraints: 14307 Sorted by residual: angle pdb=" N LEU B 81 " pdb=" CA LEU B 81 " pdb=" C LEU B 81 " ideal model delta sigma weight residual 113.23 102.23 11.00 1.24e+00 6.50e-01 7.87e+01 angle pdb=" N GLY B 71 " pdb=" CA GLY B 71 " pdb=" C GLY B 71 " ideal model delta sigma weight residual 115.32 106.68 8.64 1.38e+00 5.25e-01 3.92e+01 angle pdb=" C LEU B 68 " pdb=" N MET B 69 " pdb=" CA MET B 69 " ideal model delta sigma weight residual 123.00 115.15 7.85 1.38e+00 5.25e-01 3.23e+01 angle pdb=" N LEU B 79 " pdb=" CA LEU B 79 " pdb=" C LEU B 79 " ideal model delta sigma weight residual 113.15 107.30 5.85 1.19e+00 7.06e-01 2.42e+01 angle pdb=" N LEU A 107 " pdb=" CA LEU A 107 " pdb=" C LEU A 107 " ideal model delta sigma weight residual 112.87 107.69 5.18 1.20e+00 6.94e-01 1.87e+01 ... (remaining 14302 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 6016 34.97 - 69.93: 211 69.93 - 104.90: 34 104.90 - 139.86: 7 139.86 - 174.83: 3 Dihedral angle restraints: 6271 sinusoidal: 2513 harmonic: 3758 Sorted by residual: dihedral pdb=" C15 6OU B 602 " pdb=" C16 6OU B 602 " pdb=" O18 6OU B 602 " pdb=" C19 6OU B 602 " ideal model delta sinusoidal sigma weight residual 175.68 0.85 174.83 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C19 6OU B 602 " pdb=" C16 6OU B 602 " pdb=" O18 6OU B 602 " pdb=" O17 6OU B 602 " ideal model delta sinusoidal sigma weight residual 6.39 179.38 -172.99 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C12 6OU A 904 " pdb=" C13 6OU A 904 " pdb=" C14 6OU A 904 " pdb=" C15 6OU A 904 " ideal model delta sinusoidal sigma weight residual -173.53 -31.78 -141.75 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 6268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1248 0.043 - 0.086: 306 0.086 - 0.128: 63 0.128 - 0.171: 9 0.171 - 0.214: 4 Chirality restraints: 1630 Sorted by residual: chirality pdb=" CA VAL A 354 " pdb=" N VAL A 354 " pdb=" C VAL A 354 " pdb=" CB VAL A 354 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ILE A 352 " pdb=" N ILE A 352 " pdb=" C ILE A 352 " pdb=" CB ILE A 352 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.76e-01 chirality pdb=" C20 6OU B 601 " pdb=" C19 6OU B 601 " pdb=" C21 6OU B 601 " pdb=" O30 6OU B 601 " both_signs ideal model delta sigma weight residual False 2.35 2.53 -0.19 2.00e-01 2.50e+01 8.91e-01 ... (remaining 1627 not shown) Planarity restraints: 1817 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C39 6OU A 904 " -0.038 2.00e-02 2.50e+03 6.90e-02 4.76e+01 pdb=" C40 6OU A 904 " 0.090 2.00e-02 2.50e+03 pdb=" C41 6OU A 904 " -0.090 2.00e-02 2.50e+03 pdb=" C42 6OU A 904 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C BCT A 902 " -0.056 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" O1 BCT A 902 " 0.021 2.00e-02 2.50e+03 pdb=" O2 BCT A 902 " 0.021 2.00e-02 2.50e+03 pdb=" O3 BCT A 902 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 68 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C LEU B 68 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU B 68 " 0.021 2.00e-02 2.50e+03 pdb=" N MET B 69 " 0.019 2.00e-02 2.50e+03 ... (remaining 1814 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 68 2.58 - 3.16: 8199 3.16 - 3.74: 16501 3.74 - 4.32: 23188 4.32 - 4.90: 39712 Nonbonded interactions: 87668 Sorted by model distance: nonbonded pdb="ZN ZN A 901 " pdb=" O1 BCT A 902 " model vdw 2.005 2.230 nonbonded pdb=" OG SER A 527 " pdb=" OD2 ASP A 586 " model vdw 2.210 3.040 nonbonded pdb=" OE2 GLU A 630 " pdb=" NE2 GLN A 641 " model vdw 2.211 3.120 nonbonded pdb=" O LEU A 658 " pdb=" ND2 ASN A 661 " model vdw 2.216 3.120 nonbonded pdb=" O THR A 588 " pdb=" NH2 ARG A 625 " model vdw 2.237 3.120 ... (remaining 87663 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 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: 2.580 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.580 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10552 Z= 0.219 Angle : 0.608 11.000 14307 Z= 0.347 Chirality : 0.040 0.214 1630 Planarity : 0.004 0.069 1817 Dihedral : 18.790 174.826 3843 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.38 % Favored : 96.46 % Rotamer: Outliers : 0.95 % Allowed : 12.58 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.24), residues: 1301 helix: 1.64 (0.19), residues: 771 sheet: -0.94 (0.68), residues: 67 loop : -1.25 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 323 TYR 0.009 0.001 TYR B 34 PHE 0.014 0.001 PHE A 166 TRP 0.008 0.001 TRP A 649 HIS 0.005 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.22 (10549) covalent geometry : angle 0.60777 / 0.35 (14307) hydrogen bonds : bond 0.12545 / 8.61 ( 611) hydrogen bonds : angle 5.50506 / 3.94 ( 1788) metal coordination : bond 0.00304 / 0.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.320 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 91 average time/residue: 0.1024 time to fit residues: 13.4985 Evaluate side-chains 86 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 354 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS A 210 ASN A 709 ASN A 760 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.147703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.124658 restraints weight = 10963.708| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.29 r_work: 0.3286 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.0571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10552 Z= 0.157 Angle : 0.506 6.186 14307 Z= 0.262 Chirality : 0.039 0.199 1630 Planarity : 0.004 0.044 1817 Dihedral : 14.860 153.123 1570 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.81 % Allowed : 12.68 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.24), residues: 1301 helix: 1.68 (0.19), residues: 782 sheet: -1.23 (0.64), residues: 72 loop : -1.13 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 625 TYR 0.012 0.001 TYR B 210 PHE 0.015 0.002 PHE A 682 TRP 0.010 0.001 TRP A 230 HIS 0.005 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (10549) covalent geometry : angle 0.50615 / 0.26 (14307) hydrogen bonds : bond 0.04299 / 2.90 ( 611) hydrogen bonds : angle 4.13067 / 2.91 ( 1788) metal coordination : bond 0.00500 / 0.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.278 Fit side-chains outliers start: 19 outliers final: 18 residues processed: 103 average time/residue: 0.1072 time to fit residues: 15.5488 Evaluate side-chains 101 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 428 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 101 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 0.0770 chunk 61 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 156 HIS A 210 ASN A 760 HIS ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.149600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.126608 restraints weight = 10894.517| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.27 r_work: 0.3372 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10552 Z= 0.107 Angle : 0.442 6.048 14307 Z= 0.231 Chirality : 0.037 0.140 1630 Planarity : 0.004 0.041 1817 Dihedral : 12.645 166.477 1567 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.10 % Allowed : 13.25 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.24), residues: 1301 helix: 1.82 (0.19), residues: 796 sheet: -1.52 (0.59), residues: 77 loop : -0.88 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 517 TYR 0.011 0.001 TYR B 113 PHE 0.018 0.001 PHE A 166 TRP 0.008 0.001 TRP A 204 HIS 0.005 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (10549) covalent geometry : angle 0.44195 / 0.23 (14307) hydrogen bonds : bond 0.03685 / 2.47 ( 611) hydrogen bonds : angle 3.82549 / 2.67 ( 1788) metal coordination : bond 0.00490 / 0.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.352 Fit side-chains outliers start: 22 outliers final: 15 residues processed: 108 average time/residue: 0.1023 time to fit residues: 16.2968 Evaluate side-chains 99 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 428 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 53 optimal weight: 6.9990 chunk 55 optimal weight: 0.0000 chunk 15 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 43 optimal weight: 0.9980 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 156 HIS A 210 ASN A 606 GLN A 760 HIS ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.149178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.126238 restraints weight = 10992.777| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.28 r_work: 0.3344 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10552 Z= 0.114 Angle : 0.447 6.089 14307 Z= 0.231 Chirality : 0.037 0.139 1630 Planarity : 0.004 0.038 1817 Dihedral : 11.567 168.658 1565 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.43 % Allowed : 12.77 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.24), residues: 1301 helix: 1.85 (0.19), residues: 802 sheet: -1.46 (0.60), residues: 77 loop : -0.83 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 625 TYR 0.012 0.001 TYR B 113 PHE 0.016 0.001 PHE A 166 TRP 0.007 0.001 TRP B 44 HIS 0.005 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (10549) covalent geometry : angle 0.44703 / 0.23 (14307) hydrogen bonds : bond 0.03604 / 2.41 ( 611) hydrogen bonds : angle 3.72860 / 2.60 ( 1788) metal coordination : bond 0.00422 / 0.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 0.368 Fit side-chains REVERT: B 238 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.5873 (mm-40) outliers start: 36 outliers final: 25 residues processed: 113 average time/residue: 0.0998 time to fit residues: 16.4470 Evaluate side-chains 110 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 569 GLU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 802 MET Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 238 GLN Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 428 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 3 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 36 optimal weight: 0.1980 chunk 29 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 156 HIS A 210 ASN A 760 HIS ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.150868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.127442 restraints weight = 10928.081| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.30 r_work: 0.3327 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10552 Z= 0.108 Angle : 0.437 6.008 14307 Z= 0.226 Chirality : 0.037 0.133 1630 Planarity : 0.004 0.036 1817 Dihedral : 10.723 126.411 1565 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.05 % Allowed : 13.54 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.24), residues: 1301 helix: 1.93 (0.19), residues: 803 sheet: -1.43 (0.60), residues: 77 loop : -0.75 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 360 TYR 0.016 0.001 TYR B 113 PHE 0.016 0.001 PHE A 166 TRP 0.007 0.001 TRP A 155 HIS 0.005 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (10549) covalent geometry : angle 0.43706 / 0.23 (14307) hydrogen bonds : bond 0.03500 / 2.34 ( 611) hydrogen bonds : angle 3.66565 / 2.56 ( 1788) metal coordination : bond 0.00333 / 0.17 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 0.265 Fit side-chains REVERT: B 238 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.5878 (mm-40) outliers start: 32 outliers final: 25 residues processed: 110 average time/residue: 0.0853 time to fit residues: 13.8026 Evaluate side-chains 109 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 238 GLN Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 428 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 83 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 69 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 210 ASN A 760 HIS A 798 ASN ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.144925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.122016 restraints weight = 11201.871| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.28 r_work: 0.3262 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10552 Z= 0.217 Angle : 0.558 6.902 14307 Z= 0.285 Chirality : 0.042 0.152 1630 Planarity : 0.005 0.043 1817 Dihedral : 10.791 112.076 1565 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.24 % Allowed : 14.68 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.24), residues: 1301 helix: 1.53 (0.19), residues: 799 sheet: -1.38 (0.62), residues: 72 loop : -0.95 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 625 TYR 0.020 0.002 TYR B 113 PHE 0.023 0.002 PHE A 203 TRP 0.009 0.002 TRP A 801 HIS 0.006 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.22 (10549) covalent geometry : angle 0.55772 / 0.28 (14307) hydrogen bonds : bond 0.04500 / 3.04 ( 611) hydrogen bonds : angle 3.97118 / 2.79 ( 1788) metal coordination : bond 0.00556 / 0.29 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 0.362 Fit side-chains REVERT: B 238 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.6202 (mm-40) outliers start: 34 outliers final: 26 residues processed: 115 average time/residue: 0.0954 time to fit residues: 16.0699 Evaluate side-chains 113 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 569 GLU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 GLN Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 452 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 46 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 83 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 77 optimal weight: 0.0870 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 210 ASN A 760 HIS ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.149252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.125384 restraints weight = 10875.383| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.38 r_work: 0.3298 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10552 Z= 0.116 Angle : 0.452 6.645 14307 Z= 0.234 Chirality : 0.037 0.137 1630 Planarity : 0.004 0.038 1817 Dihedral : 10.071 99.723 1565 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.67 % Allowed : 15.63 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.24), residues: 1301 helix: 1.79 (0.19), residues: 806 sheet: -1.56 (0.58), residues: 77 loop : -0.74 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 323 TYR 0.016 0.001 TYR B 113 PHE 0.018 0.001 PHE A 166 TRP 0.010 0.001 TRP A 155 HIS 0.005 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (10549) covalent geometry : angle 0.45236 / 0.23 (14307) hydrogen bonds : bond 0.03635 / 2.43 ( 611) hydrogen bonds : angle 3.72495 / 2.61 ( 1788) metal coordination : bond 0.00426 / 0.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.373 Fit side-chains REVERT: B 238 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.5903 (mm-40) outliers start: 28 outliers final: 23 residues processed: 112 average time/residue: 0.0974 time to fit residues: 15.9854 Evaluate side-chains 112 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 GLN Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 428 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 117 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 210 ASN A 606 GLN A 760 HIS ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.149187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.125454 restraints weight = 10911.596| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.36 r_work: 0.3297 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10552 Z= 0.126 Angle : 0.461 6.152 14307 Z= 0.239 Chirality : 0.038 0.135 1630 Planarity : 0.004 0.038 1817 Dihedral : 9.843 98.522 1565 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.96 % Allowed : 15.63 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.24), residues: 1301 helix: 1.90 (0.19), residues: 800 sheet: -1.53 (0.59), residues: 77 loop : -0.77 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 323 TYR 0.018 0.001 TYR B 113 PHE 0.016 0.001 PHE A 166 TRP 0.008 0.001 TRP A 155 HIS 0.005 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (10549) covalent geometry : angle 0.46068 / 0.24 (14307) hydrogen bonds : bond 0.03696 / 2.47 ( 611) hydrogen bonds : angle 3.69809 / 2.59 ( 1788) metal coordination : bond 0.00359 / 0.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 0.366 Fit side-chains REVERT: B 238 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.5965 (mm-40) outliers start: 31 outliers final: 28 residues processed: 112 average time/residue: 0.1007 time to fit residues: 16.3937 Evaluate side-chains 116 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 569 GLU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 GLN Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 428 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 91 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 84 optimal weight: 0.0370 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 42 optimal weight: 0.0370 chunk 122 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 126 optimal weight: 0.0270 chunk 45 optimal weight: 0.0670 chunk 78 optimal weight: 3.9990 overall best weight: 0.1532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 210 ASN A 240 GLN A 606 GLN A 760 HIS ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.153790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.130804 restraints weight = 10831.874| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.23 r_work: 0.3416 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10552 Z= 0.083 Angle : 0.416 7.098 14307 Z= 0.216 Chirality : 0.036 0.135 1630 Planarity : 0.004 0.038 1817 Dihedral : 9.101 97.987 1565 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.10 % Allowed : 16.49 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.24), residues: 1301 helix: 2.14 (0.19), residues: 804 sheet: -1.67 (0.57), residues: 80 loop : -0.64 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 564 TYR 0.012 0.001 TYR B 113 PHE 0.018 0.001 PHE A 166 TRP 0.013 0.001 TRP A 155 HIS 0.004 0.000 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00171 / 0.08 (10549) covalent geometry : angle 0.41581 / 0.22 (14307) hydrogen bonds : bond 0.03114 / 2.05 ( 611) hydrogen bonds : angle 3.51039 / 2.46 ( 1788) metal coordination : bond 0.00262 / 0.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 69 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7289 (p0) outliers start: 22 outliers final: 15 residues processed: 115 average time/residue: 0.0975 time to fit residues: 16.5288 Evaluate side-chains 106 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 428 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 120 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 4 optimal weight: 0.0470 chunk 19 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 85 optimal weight: 0.0770 chunk 48 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 606 GLN A 760 HIS ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.150772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.127266 restraints weight = 10779.209| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.33 r_work: 0.3317 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10552 Z= 0.116 Angle : 0.446 6.181 14307 Z= 0.230 Chirality : 0.038 0.135 1630 Planarity : 0.004 0.036 1817 Dihedral : 9.053 97.627 1565 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.00 % Allowed : 16.97 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.24), residues: 1301 helix: 2.12 (0.19), residues: 801 sheet: -1.62 (0.58), residues: 80 loop : -0.62 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 323 TYR 0.017 0.001 TYR B 113 PHE 0.015 0.001 PHE A 166 TRP 0.010 0.001 TRP A 155 HIS 0.005 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (10549) covalent geometry : angle 0.44622 / 0.23 (14307) hydrogen bonds : bond 0.03466 / 2.31 ( 611) hydrogen bonds : angle 3.57149 / 2.50 ( 1788) metal coordination : bond 0.00284 / 0.15 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.386 Fit side-chains outliers start: 21 outliers final: 20 residues processed: 102 average time/residue: 0.0916 time to fit residues: 14.0415 Evaluate side-chains 106 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 569 GLU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 460 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 126 optimal weight: 1.9990 chunk 77 optimal weight: 0.0980 chunk 100 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 606 GLN A 760 HIS ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.151849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.128263 restraints weight = 10869.668| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.34 r_work: 0.3345 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10552 Z= 0.099 Angle : 0.436 7.343 14307 Z= 0.224 Chirality : 0.037 0.131 1630 Planarity : 0.004 0.035 1817 Dihedral : 8.849 97.178 1565 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.91 % Allowed : 17.45 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.24), residues: 1301 helix: 2.17 (0.19), residues: 800 sheet: -1.60 (0.58), residues: 80 loop : -0.60 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 323 TYR 0.017 0.001 TYR B 113 PHE 0.016 0.001 PHE A 166 TRP 0.010 0.001 TRP A 155 HIS 0.005 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (10549) covalent geometry : angle 0.43614 / 0.22 (14307) hydrogen bonds : bond 0.03328 / 2.22 ( 611) hydrogen bonds : angle 3.53739 / 2.48 ( 1788) metal coordination : bond 0.00234 / 0.12 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2329.79 seconds wall clock time: 40 minutes 41.05 seconds (2441.05 seconds total)