Starting phenix.real_space_refine on Thu Jun 4 05:47:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rd0_53925/06_2026/9rd0_53925.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rd0_53925/06_2026/9rd0_53925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rd0_53925/06_2026/9rd0_53925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rd0_53925/06_2026/9rd0_53925.map" model { file = "/net/cci-nas-00/data/ceres_data/9rd0_53925/06_2026/9rd0_53925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rd0_53925/06_2026/9rd0_53925.cif" } resolution = 2.6 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= 0.032 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 6712 2.51 5 N 1815 2.21 5 O 2123 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 10686 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6251 Classifications: {'peptide': 796} Link IDs: {'PTRANS': 35, 'TRANS': 760} 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: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 65 Unusual residues: {' ZN': 1, '6OU': 1, 'CO2': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 133 Unusual residues: {'6OU': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 184 Classifications: {'water': 184} Link IDs: {None: 183} Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2563 SG CYS A 351 42.798 57.358 36.325 1.00 26.46 S ATOM 4004 SG CYS A 539 45.192 57.480 39.499 1.00 18.62 S Time building chain proxies: 2.65, per 1000 atoms: 0.25 Number of scatterers: 10686 At special positions: 0 Unit cell: (82.49, 94.9, 125.56, 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 2123 8.00 N 1815 7.00 C 6712 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 503.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 539 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 351 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 524 " 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2446 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 6 sheets defined 67.3% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 10 through 26 Processing helix chain 'A' and resid 33 through 37 removed outlier: 3.727A pdb=" N PHE A 37 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 47 removed outlier: 3.869A pdb=" N ILE A 47 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 62 Processing helix chain 'A' and resid 69 through 78 removed outlier: 3.664A pdb=" N PHE A 73 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A 76 " --> pdb=" O TRP A 72 " (cutoff:3.500A) removed outlier: 3.577A 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: 3.598A 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 179 through 183 Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.649A pdb=" N LEU A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) 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 244 removed outlier: 3.610A pdb=" N HIS A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 268 removed outlier: 3.574A pdb=" N GLU A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 286 Processing helix chain 'A' and resid 300 through 329 removed outlier: 4.312A pdb=" N ARG A 324 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE A 325 " --> pdb=" O PHE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 367 removed outlier: 3.735A pdb=" N GLU A 357 " --> pdb=" O ASP A 353 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL A 358 " --> pdb=" O VAL A 354 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE A 359 " --> pdb=" O ARG A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 435 removed outlier: 3.501A 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: 3.759A 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 538 Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 560 through 569 removed outlier: 3.531A pdb=" N ILE A 568 " --> pdb=" O ARG A 564 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 626 Processing helix chain 'A' and resid 627 through 629 No H-bonds generated for 'chain 'A' and resid 627 through 629' Processing helix chain 'A' and resid 637 through 648 Processing helix chain 'A' and resid 668 through 673 removed outlier: 4.086A pdb=" N THR A 672 " --> pdb=" O PRO A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 693 removed outlier: 6.219A pdb=" N LYS A 692 " --> pdb=" O ARG A 689 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLU A 693 " --> pdb=" O HIS A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 703 Processing helix chain 'A' and resid 703 through 721 removed outlier: 3.533A 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 757 through 759 No H-bonds generated for 'chain 'A' and resid 757 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 24 Proline residue: B 17 - end of helix removed outlier: 3.941A 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 76 through 82 removed outlier: 3.501A pdb=" N LEU B 81 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 114 removed outlier: 4.080A 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 Processing helix chain 'B' and resid 167 through 200 removed outlier: 3.686A 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: 3.586A 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 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'B' and resid 265 through 274 removed outlier: 3.621A pdb=" N VAL B 271 " --> pdb=" O GLY B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 281 Processing helix chain 'B' and resid 281 through 304 removed outlier: 4.149A pdb=" N LEU B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 3.512A 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 Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 373 through 395 Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.994A pdb=" N GLN B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N MET B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HIS B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 457 removed outlier: 3.563A pdb=" N PHE B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 491 removed outlier: 3.566A pdb=" N ASP B 472 " --> pdb=" O ALA B 468 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 473 " --> pdb=" O PRO B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 496 removed outlier: 4.087A pdb=" N THR B 495 " --> pdb=" O GLY B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 511 Processing helix chain 'B' and resid 514 through 527 removed outlier: 3.581A pdb=" N TRP B 518 " --> pdb=" O TYR B 514 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 371 through 375 removed outlier: 6.181A pdb=" N VAL A 346 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE A 373 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA A 348 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N PHE A 375 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N PHE A 350 " --> pdb=" O PHE A 375 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N CYS A 351 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N HIS A 524 " --> pdb=" O CYS A 351 " (cutoff:3.500A) removed outlier: 4.209A 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: 6.201A pdb=" N ASP A 384 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N GLU A 409 " --> pdb=" O ASP A 384 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N CYS A 386 " --> pdb=" O GLU A 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 681 through 684 removed outlier: 6.364A pdb=" N PHE A 664 " --> pdb=" O TYR A 775 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALA A 774 " --> pdb=" O LEU A 805 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE A 807 " --> pdb=" O ALA A 774 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE A 776 " --> pdb=" O ILE A 807 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE A 804 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASP A 821 " --> pdb=" O HIS A 817 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 726 through 728 Processing sheet with id=AA5, first strand: chain 'A' and resid 733 through 736 Processing sheet with id=AA6, first strand: chain 'B' and resid 68 through 69 644 hydrogen bonds defined for protein. 1881 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: 1.98 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1870 1.33 - 1.45: 2674 1.45 - 1.57: 6039 1.57 - 1.69: 8 1.69 - 1.81: 55 Bond restraints: 10646 Sorted by residual: bond pdb=" C CO2 A 903 " pdb=" O2 CO2 A 903 " ideal model delta sigma weight residual 1.155 1.221 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C CO2 A 905 " pdb=" O2 CO2 A 905 " ideal model delta sigma weight residual 1.155 1.220 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C CO2 A 906 " pdb=" O1 CO2 A 906 " ideal model delta sigma weight residual 1.155 1.220 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C CO2 A 906 " pdb=" O2 CO2 A 906 " ideal model delta sigma weight residual 1.155 1.220 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C CO2 A 907 " pdb=" O2 CO2 A 907 " ideal model delta sigma weight residual 1.155 1.220 -0.065 2.00e-02 2.50e+03 1.05e+01 ... (remaining 10641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 14324 2.08 - 4.16: 86 4.16 - 6.24: 13 6.24 - 8.31: 4 8.31 - 10.39: 1 Bond angle restraints: 14428 Sorted by residual: angle pdb=" N PRO B 371 " pdb=" CD PRO B 371 " pdb=" CG PRO B 371 " ideal model delta sigma weight residual 103.20 97.67 5.53 1.50e+00 4.44e-01 1.36e+01 angle pdb=" CA PRO B 371 " pdb=" N PRO B 371 " pdb=" CD PRO B 371 " ideal model delta sigma weight residual 112.00 107.03 4.97 1.40e+00 5.10e-01 1.26e+01 angle pdb=" CB PRO B 371 " pdb=" CG PRO B 371 " pdb=" CD PRO B 371 " ideal model delta sigma weight residual 106.10 95.71 10.39 3.20e+00 9.77e-02 1.05e+01 angle pdb=" CA PRO B 371 " pdb=" CB PRO B 371 " pdb=" CG PRO B 371 " ideal model delta sigma weight residual 104.50 99.87 4.63 1.90e+00 2.77e-01 5.94e+00 angle pdb=" C GLY A 151 " pdb=" N GLN A 152 " pdb=" CA GLN A 152 " ideal model delta sigma weight residual 122.15 128.59 -6.44 2.83e+00 1.25e-01 5.18e+00 ... (remaining 14423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.32: 5915 29.32 - 58.64: 359 58.64 - 87.96: 40 87.96 - 117.28: 5 117.28 - 146.61: 5 Dihedral angle restraints: 6324 sinusoidal: 2539 harmonic: 3785 Sorted by residual: dihedral pdb=" C19 6OU B 603 " pdb=" C16 6OU B 603 " pdb=" O18 6OU B 603 " pdb=" O17 6OU B 603 " ideal model delta sinusoidal sigma weight residual 6.39 -140.22 146.61 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" C15 6OU B 603 " pdb=" C16 6OU B 603 " pdb=" O18 6OU B 603 " pdb=" C19 6OU B 603 " ideal model delta sinusoidal sigma weight residual 175.68 -39.72 -144.60 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" C19 6OU A 908 " pdb=" C20 6OU A 908 " pdb=" C21 6OU A 908 " pdb=" O22 6OU A 908 " ideal model delta sinusoidal sigma weight residual -59.00 68.81 -127.81 1 3.00e+01 1.11e-03 1.72e+01 ... (remaining 6321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1017 0.025 - 0.050: 360 0.050 - 0.074: 186 0.074 - 0.099: 56 0.099 - 0.124: 23 Chirality restraints: 1642 Sorted by residual: chirality pdb=" CA ILE A 812 " pdb=" N ILE A 812 " pdb=" C ILE A 812 " pdb=" CB ILE A 812 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CA ILE A 807 " pdb=" N ILE A 807 " pdb=" C ILE A 807 " pdb=" CB ILE A 807 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.59e-01 chirality pdb=" CA VAL A 194 " pdb=" N VAL A 194 " pdb=" C VAL A 194 " pdb=" CB VAL A 194 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.55e-01 ... (remaining 1639 not shown) Planarity restraints: 1829 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 712 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C ASN A 712 " -0.034 2.00e-02 2.50e+03 pdb=" O ASN A 712 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU A 713 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 710 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C TRP A 710 " 0.033 2.00e-02 2.50e+03 pdb=" O TRP A 710 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE A 711 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 711 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.33e+00 pdb=" C ILE A 711 " 0.032 2.00e-02 2.50e+03 pdb=" O ILE A 711 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN A 712 " -0.011 2.00e-02 2.50e+03 ... (remaining 1826 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1806 2.76 - 3.30: 10064 3.30 - 3.83: 19677 3.83 - 4.37: 24545 4.37 - 4.90: 40225 Nonbonded interactions: 96317 Sorted by model distance: nonbonded pdb=" O ASP A 538 " pdb=" O HOH A1001 " model vdw 2.227 3.040 nonbonded pdb=" O ARG B 108 " pdb=" O HOH B 701 " model vdw 2.265 3.040 nonbonded pdb=" OD1 ASP B 281 " pdb=" O HOH B 702 " model vdw 2.270 3.040 nonbonded pdb=" OG SER A 527 " pdb=" OD2 ASP A 586 " model vdw 2.272 3.040 nonbonded pdb=" O LEU A 658 " pdb=" ND2 ASN A 661 " model vdw 2.277 3.120 ... (remaining 96312 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: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.580 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 0.066 10649 Z= 0.145 Angle : 0.456 10.393 14428 Z= 0.238 Chirality : 0.035 0.124 1642 Planarity : 0.004 0.041 1829 Dihedral : 18.501 146.606 3878 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.37 % Favored : 97.56 % Rotamer: Outliers : 0.47 % Allowed : 18.64 % Favored : 80.89 % 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: 1.46 (0.23), residues: 1310 helix: 1.63 (0.18), residues: 815 sheet: 0.19 (0.57), residues: 78 loop : -0.08 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 501 TYR 0.007 0.001 TYR B 34 PHE 0.013 0.001 PHE A 143 TRP 0.012 0.001 TRP B 44 HIS 0.006 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (10646) covalent geometry : angle 0.45635 / 0.24 (14428) hydrogen bonds : bond 0.13081 / 8.86 ( 644) hydrogen bonds : angle 5.65824 / 4.20 ( 1881) metal coordination : bond 0.00096 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 124 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 22 ASP cc_start: 0.7317 (m-30) cc_final: 0.6973 (m-30) REVERT: A 640 LYS cc_start: 0.7581 (ttpp) cc_final: 0.7157 (ttpp) outliers start: 5 outliers final: 2 residues processed: 127 average time/residue: 0.6997 time to fit residues: 94.7064 Evaluate side-chains 123 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 121 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 443 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 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 49 GLN A 152 GLN A 330 ASN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 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 = 0.3776 r_free = 0.3776 target = 0.148274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.120978 restraints weight = 10420.774| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.23 r_work: 0.3491 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10649 Z= 0.221 Angle : 0.609 9.391 14428 Z= 0.316 Chirality : 0.042 0.201 1642 Planarity : 0.005 0.052 1829 Dihedral : 12.738 127.396 1586 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 5.11 % Allowed : 13.62 % Favored : 81.27 % 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 (0.23), residues: 1310 helix: 1.76 (0.18), residues: 828 sheet: -0.02 (0.56), residues: 78 loop : -0.28 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 625 TYR 0.016 0.003 TYR A 172 PHE 0.023 0.003 PHE A 166 TRP 0.014 0.002 TRP B 44 HIS 0.009 0.001 HIS A 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.22 (10646) covalent geometry : angle 0.60904 / 0.32 (14428) hydrogen bonds : bond 0.05776 / 3.85 ( 644) hydrogen bonds : angle 4.22814 / 3.19 ( 1881) metal coordination : bond 0.00103 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 123 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 189 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.6644 (mp-120) REVERT: A 236 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.6457 (t80) REVERT: A 569 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6844 (mm-30) REVERT: B 27 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.8006 (tttp) outliers start: 54 outliers final: 28 residues processed: 157 average time/residue: 0.6725 time to fit residues: 112.8678 Evaluate side-chains 147 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 569 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 515 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 127 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.151566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.124338 restraints weight = 10260.525| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.24 r_work: 0.3416 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10649 Z= 0.164 Angle : 0.537 8.613 14428 Z= 0.279 Chirality : 0.039 0.143 1642 Planarity : 0.005 0.052 1829 Dihedral : 12.120 117.492 1584 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.35 % Allowed : 14.00 % Favored : 81.65 % 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: 1.64 (0.23), residues: 1310 helix: 1.87 (0.18), residues: 829 sheet: 0.08 (0.57), residues: 73 loop : -0.30 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 625 TYR 0.013 0.002 TYR B 446 PHE 0.020 0.002 PHE A 166 TRP 0.013 0.001 TRP B 44 HIS 0.009 0.001 HIS A 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (10646) covalent geometry : angle 0.53698 / 0.28 (14428) hydrogen bonds : bond 0.04969 / 3.31 ( 644) hydrogen bonds : angle 4.02518 / 3.04 ( 1881) metal coordination : bond 0.00113 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 128 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 22 ASP cc_start: 0.7296 (m-30) cc_final: 0.6981 (m-30) REVERT: A 180 SER cc_start: 0.8078 (OUTLIER) cc_final: 0.7846 (m) REVERT: A 189 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.6566 (mp-120) REVERT: A 202 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7868 (tp) REVERT: A 236 TYR cc_start: 0.8921 (OUTLIER) cc_final: 0.6389 (t80) REVERT: A 714 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.7115 (tp40) REVERT: B 27 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8035 (tttp) outliers start: 46 outliers final: 27 residues processed: 158 average time/residue: 0.6620 time to fit residues: 111.9037 Evaluate side-chains 154 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 515 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 2 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.156496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.129413 restraints weight = 10132.001| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.24 r_work: 0.3463 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10649 Z= 0.125 Angle : 0.493 8.420 14428 Z= 0.256 Chirality : 0.037 0.139 1642 Planarity : 0.004 0.051 1829 Dihedral : 11.444 118.860 1584 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.35 % Allowed : 14.47 % Favored : 81.17 % 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: 1.85 (0.23), residues: 1310 helix: 2.05 (0.18), residues: 829 sheet: 0.07 (0.58), residues: 73 loop : -0.23 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 625 TYR 0.011 0.002 TYR B 446 PHE 0.018 0.002 PHE A 166 TRP 0.012 0.001 TRP B 44 HIS 0.007 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (10646) covalent geometry : angle 0.49344 / 0.26 (14428) hydrogen bonds : bond 0.04391 / 2.92 ( 644) hydrogen bonds : angle 3.89455 / 2.94 ( 1881) metal coordination : bond 0.00072 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 125 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 22 ASP cc_start: 0.7297 (m-30) cc_final: 0.6980 (m-30) REVERT: A 202 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7855 (tp) REVERT: A 236 TYR cc_start: 0.8894 (OUTLIER) cc_final: 0.6231 (t80) REVERT: A 569 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6902 (mm-30) REVERT: A 714 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7117 (tp40) REVERT: A 764 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7770 (pt0) REVERT: B 27 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.8050 (tttp) outliers start: 46 outliers final: 24 residues processed: 154 average time/residue: 0.6531 time to fit residues: 107.7249 Evaluate side-chains 152 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 569 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 515 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 49 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN ** A 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.158493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.131525 restraints weight = 10076.590| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.24 r_work: 0.3516 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10649 Z= 0.104 Angle : 0.460 7.981 14428 Z= 0.238 Chirality : 0.036 0.134 1642 Planarity : 0.004 0.049 1829 Dihedral : 10.897 121.592 1584 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.16 % Allowed : 14.85 % Favored : 80.98 % 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: 2.09 (0.24), residues: 1310 helix: 2.24 (0.18), residues: 829 sheet: 0.17 (0.59), residues: 73 loop : -0.13 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 625 TYR 0.010 0.001 TYR B 446 PHE 0.016 0.002 PHE A 166 TRP 0.012 0.001 TRP B 44 HIS 0.010 0.001 HIS A 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (10646) covalent geometry : angle 0.45978 / 0.24 (14428) hydrogen bonds : bond 0.03905 / 2.60 ( 644) hydrogen bonds : angle 3.75971 / 2.84 ( 1881) metal coordination : bond 0.00064 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 22 ASP cc_start: 0.7218 (m-30) cc_final: 0.6887 (m-30) REVERT: A 48 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7873 (p0) REVERT: A 202 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7842 (tp) REVERT: A 236 TYR cc_start: 0.8842 (OUTLIER) cc_final: 0.6158 (t80) REVERT: A 311 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8161 (tt0) REVERT: A 569 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6887 (mm-30) REVERT: A 612 GLN cc_start: 0.7589 (tm-30) cc_final: 0.7310 (tm-30) REVERT: A 714 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7068 (tp40) REVERT: A 764 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7708 (pt0) outliers start: 44 outliers final: 22 residues processed: 154 average time/residue: 0.6726 time to fit residues: 110.8170 Evaluate side-chains 153 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 569 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 476 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 109 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 chunk 74 optimal weight: 0.2980 chunk 36 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.152776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.125985 restraints weight = 10451.327| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.20 r_work: 0.3522 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10649 Z= 0.142 Angle : 0.508 8.816 14428 Z= 0.263 Chirality : 0.038 0.146 1642 Planarity : 0.004 0.050 1829 Dihedral : 11.015 123.800 1584 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.82 % Allowed : 14.00 % Favored : 81.17 % 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: 1.96 (0.23), residues: 1310 helix: 2.14 (0.18), residues: 829 sheet: 0.10 (0.59), residues: 73 loop : -0.20 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 625 TYR 0.013 0.002 TYR B 446 PHE 0.019 0.002 PHE A 166 TRP 0.011 0.001 TRP B 44 HIS 0.010 0.001 HIS A 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (10646) covalent geometry : angle 0.50752 / 0.26 (14428) hydrogen bonds : bond 0.04514 / 3.00 ( 644) hydrogen bonds : angle 3.84174 / 2.90 ( 1881) metal coordination : bond 0.00074 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 127 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 22 ASP cc_start: 0.7400 (m-30) cc_final: 0.7105 (m-30) REVERT: A 189 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.6642 (mp-120) REVERT: A 202 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8023 (tp) REVERT: A 236 TYR cc_start: 0.8924 (OUTLIER) cc_final: 0.6338 (t80) REVERT: A 311 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8330 (tt0) REVERT: A 569 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6951 (mm-30) REVERT: A 714 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7153 (tp40) REVERT: B 27 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8076 (tttp) outliers start: 51 outliers final: 24 residues processed: 159 average time/residue: 0.6662 time to fit residues: 113.4161 Evaluate side-chains 155 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 569 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 476 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 118 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 108 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 60 optimal weight: 0.0970 chunk 64 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN ** A 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.155654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.129137 restraints weight = 10368.576| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.20 r_work: 0.3508 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10649 Z= 0.102 Angle : 0.456 7.888 14428 Z= 0.236 Chirality : 0.036 0.132 1642 Planarity : 0.004 0.049 1829 Dihedral : 10.635 124.261 1584 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.31 % Allowed : 15.33 % Favored : 81.36 % 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: 2.17 (0.24), residues: 1310 helix: 2.32 (0.18), residues: 829 sheet: 0.18 (0.59), residues: 73 loop : -0.13 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 815 TYR 0.009 0.001 TYR B 446 PHE 0.016 0.002 PHE A 166 TRP 0.011 0.001 TRP B 44 HIS 0.007 0.001 HIS A 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (10646) covalent geometry : angle 0.45624 / 0.24 (14428) hydrogen bonds : bond 0.03797 / 2.53 ( 644) hydrogen bonds : angle 3.72277 / 2.82 ( 1881) metal coordination : bond 0.00072 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 22 ASP cc_start: 0.7322 (m-30) cc_final: 0.7014 (m-30) REVERT: A 189 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.6556 (mp-120) REVERT: A 236 TYR cc_start: 0.8848 (OUTLIER) cc_final: 0.6118 (t80) REVERT: A 311 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8225 (tt0) REVERT: A 612 GLN cc_start: 0.7700 (tm-30) cc_final: 0.7431 (tm-30) REVERT: A 714 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7107 (tp40) outliers start: 35 outliers final: 22 residues processed: 148 average time/residue: 0.7180 time to fit residues: 113.4781 Evaluate side-chains 147 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 476 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 71 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 117 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN ** A 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.154009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.127259 restraints weight = 10348.889| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.20 r_work: 0.3484 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10649 Z= 0.124 Angle : 0.486 8.517 14428 Z= 0.252 Chirality : 0.037 0.146 1642 Planarity : 0.004 0.050 1829 Dihedral : 10.669 124.463 1584 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.69 % Allowed : 14.95 % Favored : 81.36 % 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: 2.11 (0.23), residues: 1310 helix: 2.26 (0.18), residues: 829 sheet: 0.13 (0.59), residues: 73 loop : -0.12 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 815 TYR 0.012 0.002 TYR B 446 PHE 0.018 0.002 PHE A 166 TRP 0.011 0.001 TRP B 44 HIS 0.008 0.001 HIS A 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (10646) covalent geometry : angle 0.48612 / 0.25 (14428) hydrogen bonds : bond 0.04199 / 2.79 ( 644) hydrogen bonds : angle 3.76089 / 2.84 ( 1881) metal coordination : bond 0.00067 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 22 ASP cc_start: 0.7340 (m-30) cc_final: 0.7040 (m-30) REVERT: A 189 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.6656 (mp-120) REVERT: A 236 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.6168 (t80) REVERT: A 311 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: A 324 ARG cc_start: 0.7712 (mtt180) cc_final: 0.7461 (mtt180) REVERT: A 714 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7099 (tp40) REVERT: B 27 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.8056 (tttp) outliers start: 39 outliers final: 24 residues processed: 148 average time/residue: 0.7052 time to fit residues: 111.6787 Evaluate side-chains 149 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 497 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 116 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN ** A 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.150829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.124076 restraints weight = 10348.424| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.20 r_work: 0.3447 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10649 Z= 0.200 Angle : 0.577 9.177 14428 Z= 0.299 Chirality : 0.041 0.156 1642 Planarity : 0.005 0.051 1829 Dihedral : 11.210 124.264 1584 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.88 % Allowed : 14.76 % Favored : 81.36 % 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: 1.74 (0.23), residues: 1310 helix: 1.96 (0.18), residues: 829 sheet: -0.01 (0.58), residues: 73 loop : -0.24 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 625 TYR 0.016 0.003 TYR A 172 PHE 0.023 0.003 PHE A 166 TRP 0.011 0.002 TRP A 670 HIS 0.010 0.001 HIS A 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (10646) covalent geometry : angle 0.57718 / 0.30 (14428) hydrogen bonds : bond 0.05309 / 3.52 ( 644) hydrogen bonds : angle 3.97676 / 3.01 ( 1881) metal coordination : bond 0.00064 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 120 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 22 ASP cc_start: 0.7434 (m-30) cc_final: 0.7118 (m-30) REVERT: A 189 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.6654 (mp-120) REVERT: A 236 TYR cc_start: 0.8962 (OUTLIER) cc_final: 0.6387 (t80) REVERT: A 714 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7160 (tp40) outliers start: 41 outliers final: 23 residues processed: 147 average time/residue: 0.6929 time to fit residues: 108.7559 Evaluate side-chains 143 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 476 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 0.0570 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN ** A 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 490 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.155030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.128519 restraints weight = 10285.260| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.19 r_work: 0.3506 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10649 Z= 0.105 Angle : 0.468 7.965 14428 Z= 0.243 Chirality : 0.036 0.131 1642 Planarity : 0.004 0.049 1829 Dihedral : 10.729 123.666 1584 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.93 % Allowed : 15.61 % Favored : 81.46 % 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: 2.10 (0.24), residues: 1310 helix: 2.24 (0.18), residues: 829 sheet: 0.13 (0.58), residues: 73 loop : -0.10 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 815 TYR 0.009 0.001 TYR B 34 PHE 0.015 0.001 PHE A 166 TRP 0.012 0.001 TRP B 44 HIS 0.007 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (10646) covalent geometry : angle 0.46784 / 0.24 (14428) hydrogen bonds : bond 0.03926 / 2.62 ( 644) hydrogen bonds : angle 3.76422 / 2.85 ( 1881) metal coordination : bond 0.00163 / 0.08 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 189 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.6555 (mp-120) REVERT: A 236 TYR cc_start: 0.8861 (OUTLIER) cc_final: 0.6225 (t80) REVERT: A 714 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7128 (tp40) outliers start: 31 outliers final: 20 residues processed: 145 average time/residue: 0.7254 time to fit residues: 111.9985 Evaluate side-chains 143 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 476 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 100 optimal weight: 0.7980 chunk 94 optimal weight: 0.3980 chunk 38 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN ** A 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.154266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.127545 restraints weight = 10337.123| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.20 r_work: 0.3492 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10649 Z= 0.118 Angle : 0.482 8.345 14428 Z= 0.250 Chirality : 0.037 0.141 1642 Planarity : 0.004 0.050 1829 Dihedral : 10.624 123.494 1584 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.74 % Allowed : 16.18 % Favored : 81.08 % 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: 2.14 (0.24), residues: 1310 helix: 2.27 (0.18), residues: 829 sheet: 0.15 (0.58), residues: 73 loop : -0.07 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 815 TYR 0.011 0.002 TYR B 446 PHE 0.017 0.002 PHE A 166 TRP 0.011 0.001 TRP B 44 HIS 0.007 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (10646) covalent geometry : angle 0.48193 / 0.25 (14428) hydrogen bonds : bond 0.04118 / 2.74 ( 644) hydrogen bonds : angle 3.75397 / 2.84 ( 1881) metal coordination : bond 0.00094 / 0.05 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3879.45 seconds wall clock time: 66 minutes 53.34 seconds (4013.34 seconds total)