Starting phenix.real_space_refine on Fri May 16 16:17:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y3e_33592/05_2025/7y3e_33592.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y3e_33592/05_2025/7y3e_33592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y3e_33592/05_2025/7y3e_33592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y3e_33592/05_2025/7y3e_33592.map" model { file = "/net/cci-nas-00/data/ceres_data/7y3e_33592/05_2025/7y3e_33592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y3e_33592/05_2025/7y3e_33592.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= -0.003 sd= 0.142 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 9522 2.51 5 N 2364 2.21 5 O 2626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14572 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7254 Classifications: {'peptide': 928} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 894} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 7254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7254 Classifications: {'peptide': 928} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 894} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'R16': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'R16': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.73, per 1000 atoms: 0.60 Number of scatterers: 14572 At special positions: 0 Unit cell: (115.44, 105.04, 127.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2626 8.00 N 2364 7.00 C 9522 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: 4.20 Conformation dependent library (CDL) restraints added in 1.6 seconds 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3456 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 8 sheets defined 69.9% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 34 through 54 removed outlier: 3.625A pdb=" N LEU A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 78 removed outlier: 4.061A pdb=" N ALA A 64 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 95 Processing helix chain 'A' and resid 97 through 116 Proline residue: A 107 - end of helix removed outlier: 4.568A pdb=" N GLU A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 151 removed outlier: 5.825A pdb=" N GLY A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLN A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 172 through 184 removed outlier: 3.729A pdb=" N GLU A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 216 removed outlier: 3.672A pdb=" N ASP A 201 " --> pdb=" O SER A 197 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 253 removed outlier: 3.955A pdb=" N ALA A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 278 removed outlier: 3.597A pdb=" N THR A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR A 274 " --> pdb=" O TYR A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 299 Processing helix chain 'A' and resid 306 through 339 removed outlier: 4.357A pdb=" N SER A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 347 removed outlier: 3.784A pdb=" N GLN A 347 " --> pdb=" O ILE A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 377 Proline residue: A 374 - end of helix Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 398 through 411 Processing helix chain 'A' and resid 418 through 442 removed outlier: 3.752A pdb=" N SER A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 450 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 457 through 482 Processing helix chain 'A' and resid 492 through 500 Processing helix chain 'A' and resid 527 through 549 Processing helix chain 'A' and resid 553 through 568 Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 590 through 594 Processing helix chain 'A' and resid 603 through 638 removed outlier: 5.736A pdb=" N SER A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ALA A 615 " --> pdb=" O ARG A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 654 Processing helix chain 'A' and resid 654 through 668 removed outlier: 3.756A pdb=" N LYS A 658 " --> pdb=" O GLY A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 699 Processing helix chain 'A' and resid 704 through 723 Processing helix chain 'A' and resid 731 through 738 Processing helix chain 'A' and resid 739 through 744 removed outlier: 3.815A pdb=" N VAL A 743 " --> pdb=" O PRO A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 751 Processing helix chain 'A' and resid 810 through 817 Processing helix chain 'A' and resid 837 through 842 Processing helix chain 'A' and resid 846 through 866 removed outlier: 3.654A pdb=" N PHE A 852 " --> pdb=" O THR A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 871 removed outlier: 3.525A pdb=" N GLU A 871 " --> pdb=" O PRO A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 884 Processing helix chain 'A' and resid 1012 through 1017 removed outlier: 3.682A pdb=" N ILE A1017 " --> pdb=" O TRP A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1042 Processing helix chain 'B' and resid 34 through 54 removed outlier: 3.625A pdb=" N LEU B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 78 removed outlier: 4.061A pdb=" N ALA B 64 " --> pdb=" O PRO B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 95 Processing helix chain 'B' and resid 97 through 116 Proline residue: B 107 - end of helix removed outlier: 4.568A pdb=" N GLU B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 151 removed outlier: 5.825A pdb=" N GLY B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLN B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) Proline residue: B 135 - end of helix Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 172 through 184 removed outlier: 3.729A pdb=" N GLU B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 216 removed outlier: 3.673A pdb=" N ASP B 201 " --> pdb=" O SER B 197 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 253 removed outlier: 3.956A pdb=" N ALA B 236 " --> pdb=" O VAL B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 278 removed outlier: 3.597A pdb=" N THR B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR B 274 " --> pdb=" O TYR B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 299 Processing helix chain 'B' and resid 306 through 339 removed outlier: 4.357A pdb=" N SER B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 347 removed outlier: 3.784A pdb=" N GLN B 347 " --> pdb=" O ILE B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 377 Proline residue: B 374 - end of helix Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 398 through 411 Processing helix chain 'B' and resid 418 through 442 removed outlier: 3.752A pdb=" N SER B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 450 Processing helix chain 'B' and resid 451 through 453 No H-bonds generated for 'chain 'B' and resid 451 through 453' Processing helix chain 'B' and resid 457 through 482 Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'B' and resid 527 through 549 Processing helix chain 'B' and resid 553 through 568 Processing helix chain 'B' and resid 581 through 585 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 602 through 638 removed outlier: 4.189A pdb=" N TYR B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N SER B 614 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ALA B 615 " --> pdb=" O ARG B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 654 Processing helix chain 'B' and resid 654 through 668 removed outlier: 3.756A pdb=" N LYS B 658 " --> pdb=" O GLY B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 699 Processing helix chain 'B' and resid 704 through 723 Processing helix chain 'B' and resid 731 through 738 Processing helix chain 'B' and resid 739 through 744 removed outlier: 3.814A pdb=" N VAL B 743 " --> pdb=" O PRO B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 751 Processing helix chain 'B' and resid 810 through 817 Processing helix chain 'B' and resid 837 through 842 Processing helix chain 'B' and resid 846 through 866 removed outlier: 3.654A pdb=" N PHE B 852 " --> pdb=" O THR B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 871 removed outlier: 3.525A pdb=" N GLU B 871 " --> pdb=" O PRO B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 884 Processing helix chain 'B' and resid 1012 through 1017 removed outlier: 3.682A pdb=" N ILE B1017 " --> pdb=" O TRP B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1042 Processing sheet with id=AA1, first strand: chain 'A' and resid 761 through 762 removed outlier: 6.413A pdb=" N LEU A 831 " --> pdb=" O PHE A 782 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 767 through 769 removed outlier: 6.938A pdb=" N LEU A 824 " --> pdb=" O LEU A 768 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 888 through 892 removed outlier: 6.264A pdb=" N ARG A 966 " --> pdb=" O LEU A 909 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 913 through 914 Processing sheet with id=AA5, first strand: chain 'B' and resid 761 through 762 removed outlier: 6.413A pdb=" N LEU B 831 " --> pdb=" O PHE B 782 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 767 through 769 removed outlier: 6.938A pdb=" N LEU B 824 " --> pdb=" O LEU B 768 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 888 through 892 removed outlier: 6.264A pdb=" N ARG B 966 " --> pdb=" O LEU B 909 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 913 through 914 980 hydrogen bonds defined for protein. 2856 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: 4.74 Time building geometry restraints manager: 4.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4413 1.34 - 1.45: 2051 1.45 - 1.57: 8308 1.57 - 1.69: 0 1.69 - 1.81: 102 Bond restraints: 14874 Sorted by residual: bond pdb=" CA SER A 116 " pdb=" C SER A 116 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.41e-02 5.03e+03 3.39e+00 bond pdb=" CA SER B 116 " pdb=" C SER B 116 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.41e-02 5.03e+03 3.35e+00 bond pdb=" C PHE B 152 " pdb=" N PRO B 153 " ideal model delta sigma weight residual 1.331 1.345 -0.014 7.90e-03 1.60e+04 2.98e+00 bond pdb=" C PHE A 152 " pdb=" N PRO A 153 " ideal model delta sigma weight residual 1.331 1.345 -0.013 7.90e-03 1.60e+04 2.87e+00 bond pdb=" CG1 ILE A 361 " pdb=" CD1 ILE A 361 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.94e+00 ... (remaining 14869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 19075 1.37 - 2.74: 838 2.74 - 4.12: 160 4.12 - 5.49: 52 5.49 - 6.86: 21 Bond angle restraints: 20146 Sorted by residual: angle pdb=" N GLN A 876 " pdb=" CA GLN A 876 " pdb=" C GLN A 876 " ideal model delta sigma weight residual 113.55 107.83 5.72 1.26e+00 6.30e-01 2.06e+01 angle pdb=" N GLN B 876 " pdb=" CA GLN B 876 " pdb=" C GLN B 876 " ideal model delta sigma weight residual 113.55 107.83 5.72 1.26e+00 6.30e-01 2.06e+01 angle pdb=" N VAL B 119 " pdb=" CA VAL B 119 " pdb=" C VAL B 119 " ideal model delta sigma weight residual 110.72 114.10 -3.38 1.01e+00 9.80e-01 1.12e+01 angle pdb=" N VAL A 119 " pdb=" CA VAL A 119 " pdb=" C VAL A 119 " ideal model delta sigma weight residual 110.72 114.09 -3.37 1.01e+00 9.80e-01 1.12e+01 angle pdb=" C ILE B1041 " pdb=" N PHE B1042 " pdb=" CA PHE B1042 " ideal model delta sigma weight residual 122.12 127.94 -5.82 1.76e+00 3.23e-01 1.09e+01 ... (remaining 20141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 8021 17.87 - 35.74: 709 35.74 - 53.62: 88 53.62 - 71.49: 22 71.49 - 89.36: 18 Dihedral angle restraints: 8858 sinusoidal: 3498 harmonic: 5360 Sorted by residual: dihedral pdb=" CA ARG A 449 " pdb=" C ARG A 449 " pdb=" N LEU A 450 " pdb=" CA LEU A 450 " ideal model delta harmonic sigma weight residual 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ARG B 449 " pdb=" C ARG B 449 " pdb=" N LEU B 450 " pdb=" CA LEU B 450 " ideal model delta harmonic sigma weight residual 180.00 161.97 18.03 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA LEU A 109 " pdb=" C LEU A 109 " pdb=" N LEU A 110 " pdb=" CA LEU A 110 " ideal model delta harmonic sigma weight residual 180.00 -163.60 -16.40 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 8855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1456 0.034 - 0.068: 654 0.068 - 0.101: 209 0.101 - 0.135: 47 0.135 - 0.169: 6 Chirality restraints: 2372 Sorted by residual: chirality pdb=" CA SER A 925 " pdb=" N SER A 925 " pdb=" C SER A 925 " pdb=" CB SER A 925 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CA SER B 925 " pdb=" N SER B 925 " pdb=" C SER B 925 " pdb=" CB SER B 925 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CG LEU A 700 " pdb=" CB LEU A 700 " pdb=" CD1 LEU A 700 " pdb=" CD2 LEU A 700 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.57e-01 ... (remaining 2369 not shown) Planarity restraints: 2472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B1044 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" C SER B1044 " -0.032 2.00e-02 2.50e+03 pdb=" O SER B1044 " 0.012 2.00e-02 2.50e+03 pdb=" N MET B1045 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A1044 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.29e+00 pdb=" C SER A1044 " 0.031 2.00e-02 2.50e+03 pdb=" O SER A1044 " -0.012 2.00e-02 2.50e+03 pdb=" N MET A1045 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 774 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO B 775 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 775 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 775 " -0.024 5.00e-02 4.00e+02 ... (remaining 2469 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1210 2.74 - 3.28: 15269 3.28 - 3.82: 25266 3.82 - 4.36: 31008 4.36 - 4.90: 53542 Nonbonded interactions: 126295 Sorted by model distance: nonbonded pdb=" O VAL B 439 " pdb=" OG1 THR B 443 " model vdw 2.197 3.040 nonbonded pdb=" O VAL A 439 " pdb=" OG1 THR A 443 " model vdw 2.197 3.040 nonbonded pdb=" OE1 GLU A 470 " pdb=" OH TYR B 691 " model vdw 2.198 3.040 nonbonded pdb=" OG SER A 140 " pdb=" OG SER A 169 " model vdw 2.203 3.040 nonbonded pdb=" OG SER B 140 " pdb=" OG SER B 169 " model vdw 2.203 3.040 ... (remaining 126290 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 34.530 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 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 0.054 14874 Z= 0.196 Angle : 0.709 6.858 20146 Z= 0.392 Chirality : 0.042 0.169 2372 Planarity : 0.004 0.042 2472 Dihedral : 14.073 89.359 5402 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.20), residues: 1836 helix: 1.04 (0.15), residues: 1210 sheet: 1.67 (0.62), residues: 76 loop : -1.36 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 493 HIS 0.006 0.001 HIS A 120 PHE 0.026 0.002 PHE A 834 TYR 0.012 0.002 TYR A 590 ARG 0.008 0.001 ARG A 966 Details of bonding type rmsd hydrogen bonds : bond 0.13597 ( 980) hydrogen bonds : angle 5.95364 ( 2856) covalent geometry : bond 0.00436 (14874) covalent geometry : angle 0.70897 (20146) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.611 Fit side-chains REVERT: A 99 GLU cc_start: 0.7119 (tt0) cc_final: 0.6888 (mm-30) REVERT: A 234 LEU cc_start: 0.8220 (mp) cc_final: 0.7905 (mp) REVERT: A 375 LEU cc_start: 0.8641 (mp) cc_final: 0.8416 (mp) REVERT: A 445 GLN cc_start: 0.7672 (tp-100) cc_final: 0.7176 (mp-120) REVERT: A 449 ARG cc_start: 0.6648 (mtm110) cc_final: 0.6353 (ttp-110) REVERT: A 562 GLN cc_start: 0.7540 (tt0) cc_final: 0.7336 (tt0) REVERT: A 579 ARG cc_start: 0.7380 (ttm170) cc_final: 0.7161 (ttp80) REVERT: A 652 LYS cc_start: 0.7869 (mmtm) cc_final: 0.7613 (pttm) REVERT: A 771 GLU cc_start: 0.7561 (tt0) cc_final: 0.6874 (tt0) REVERT: B 234 LEU cc_start: 0.8243 (mp) cc_final: 0.7963 (mp) REVERT: B 375 LEU cc_start: 0.8553 (mp) cc_final: 0.8320 (mp) REVERT: B 445 GLN cc_start: 0.7682 (tp-100) cc_final: 0.7171 (mp-120) REVERT: B 449 ARG cc_start: 0.6622 (mtm110) cc_final: 0.6334 (ttp-110) REVERT: B 562 GLN cc_start: 0.7548 (tt0) cc_final: 0.7345 (tt0) REVERT: B 579 ARG cc_start: 0.7401 (ttm170) cc_final: 0.7172 (ttp80) REVERT: B 652 LYS cc_start: 0.7906 (mmtm) cc_final: 0.7605 (pttm) REVERT: B 771 GLU cc_start: 0.7605 (tt0) cc_final: 0.7078 (tt0) REVERT: B 822 CYS cc_start: 0.8250 (p) cc_final: 0.7925 (p) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 1.2584 time to fit residues: 381.5872 Evaluate side-chains 196 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.5980 chunk 139 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 0.3980 chunk 74 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 277 GLN A 347 GLN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 219 ASN B 277 GLN B 347 GLN ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.188760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.145210 restraints weight = 14820.112| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.47 r_work: 0.3487 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14874 Z= 0.214 Angle : 0.653 6.386 20146 Z= 0.336 Chirality : 0.043 0.156 2372 Planarity : 0.005 0.042 2472 Dihedral : 5.536 51.387 2020 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.69 % Allowed : 10.12 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.20), residues: 1836 helix: 1.10 (0.15), residues: 1222 sheet: 1.95 (0.60), residues: 72 loop : -1.18 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 854 HIS 0.008 0.001 HIS B 120 PHE 0.018 0.002 PHE B 607 TYR 0.018 0.002 TYR A 769 ARG 0.006 0.001 ARG A 462 Details of bonding type rmsd hydrogen bonds : bond 0.04863 ( 980) hydrogen bonds : angle 5.07516 ( 2856) covalent geometry : bond 0.00508 (14874) covalent geometry : angle 0.65271 (20146) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 213 time to evaluate : 1.649 Fit side-chains REVERT: A 234 LEU cc_start: 0.8423 (mp) cc_final: 0.8153 (mp) REVERT: A 342 ASP cc_start: 0.7893 (t0) cc_final: 0.7629 (t0) REVERT: A 375 LEU cc_start: 0.8568 (mp) cc_final: 0.8333 (mp) REVERT: A 445 GLN cc_start: 0.7909 (tp-100) cc_final: 0.7688 (mm110) REVERT: A 449 ARG cc_start: 0.6853 (mtm110) cc_final: 0.5798 (ttp-110) REVERT: A 579 ARG cc_start: 0.7795 (ttm170) cc_final: 0.7432 (ttp80) REVERT: A 652 LYS cc_start: 0.8051 (mmtm) cc_final: 0.7414 (pttm) REVERT: A 761 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7209 (tmm) REVERT: A 763 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8193 (mt) REVERT: A 866 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6834 (tpt-90) REVERT: B 234 LEU cc_start: 0.8418 (mp) cc_final: 0.8161 (mp) REVERT: B 342 ASP cc_start: 0.7832 (t0) cc_final: 0.7524 (t0) REVERT: B 375 LEU cc_start: 0.8479 (mp) cc_final: 0.8242 (mp) REVERT: B 445 GLN cc_start: 0.7888 (tp-100) cc_final: 0.7654 (mm110) REVERT: B 449 ARG cc_start: 0.6923 (mtm110) cc_final: 0.5961 (ttp-110) REVERT: B 579 ARG cc_start: 0.7809 (ttm170) cc_final: 0.7430 (ttp80) REVERT: B 652 LYS cc_start: 0.8092 (mmtm) cc_final: 0.7457 (pttm) REVERT: B 763 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8190 (mt) outliers start: 59 outliers final: 26 residues processed: 240 average time/residue: 1.2618 time to fit residues: 333.3998 Evaluate side-chains 229 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 876 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 122 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 0.2980 chunk 79 optimal weight: 0.2980 chunk 132 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 152 optimal weight: 0.8980 chunk 130 optimal weight: 0.0570 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 200 ASN A 347 GLN A 480 GLN A 537 ASN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 200 ASN B 347 GLN B 480 GLN B 537 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.192042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.150565 restraints weight = 14847.231| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.54 r_work: 0.3536 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14874 Z= 0.129 Angle : 0.547 6.248 20146 Z= 0.281 Chirality : 0.039 0.154 2372 Planarity : 0.004 0.037 2472 Dihedral : 5.093 43.950 2020 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.12 % Allowed : 12.81 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.20), residues: 1836 helix: 1.37 (0.15), residues: 1236 sheet: 1.81 (0.59), residues: 72 loop : -1.05 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 493 HIS 0.005 0.001 HIS A 626 PHE 0.016 0.002 PHE B 353 TYR 0.013 0.001 TYR A 769 ARG 0.009 0.001 ARG B 866 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 980) hydrogen bonds : angle 4.71708 ( 2856) covalent geometry : bond 0.00290 (14874) covalent geometry : angle 0.54665 (20146) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 210 time to evaluate : 1.780 Fit side-chains REVERT: A 123 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7921 (pttt) REVERT: A 221 ASP cc_start: 0.6228 (OUTLIER) cc_final: 0.5928 (p0) REVERT: A 342 ASP cc_start: 0.7889 (t0) cc_final: 0.7531 (t0) REVERT: A 449 ARG cc_start: 0.6804 (mtm110) cc_final: 0.5823 (ttp-110) REVERT: A 652 LYS cc_start: 0.8028 (mmtm) cc_final: 0.7336 (pttm) REVERT: A 763 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8090 (mt) REVERT: A 866 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6654 (tpt-90) REVERT: A 876 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7181 (pt0) REVERT: B 123 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7912 (pttt) REVERT: B 342 ASP cc_start: 0.7816 (t0) cc_final: 0.7463 (t0) REVERT: B 449 ARG cc_start: 0.6852 (mtm110) cc_final: 0.5734 (ttp-110) REVERT: B 652 LYS cc_start: 0.8021 (mmtm) cc_final: 0.7335 (pttm) REVERT: B 763 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8150 (mt) REVERT: B 771 GLU cc_start: 0.7833 (tt0) cc_final: 0.6773 (tt0) REVERT: B 966 ARG cc_start: 0.5465 (OUTLIER) cc_final: 0.5195 (ttp-170) outliers start: 50 outliers final: 15 residues processed: 234 average time/residue: 1.1299 time to fit residues: 293.0277 Evaluate side-chains 213 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 966 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 108 optimal weight: 0.9990 chunk 169 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 347 GLN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 347 GLN B 480 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.187881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.146125 restraints weight = 14717.377| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.52 r_work: 0.3454 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14874 Z= 0.190 Angle : 0.596 8.170 20146 Z= 0.303 Chirality : 0.041 0.146 2372 Planarity : 0.004 0.039 2472 Dihedral : 5.236 47.822 2020 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.38 % Allowed : 14.62 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.20), residues: 1836 helix: 1.27 (0.15), residues: 1226 sheet: 1.91 (0.61), residues: 72 loop : -0.95 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 493 HIS 0.007 0.001 HIS A 120 PHE 0.016 0.002 PHE B 314 TYR 0.013 0.002 TYR A 769 ARG 0.006 0.000 ARG B 378 Details of bonding type rmsd hydrogen bonds : bond 0.04397 ( 980) hydrogen bonds : angle 4.83388 ( 2856) covalent geometry : bond 0.00452 (14874) covalent geometry : angle 0.59570 (20146) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 212 time to evaluate : 1.533 Fit side-chains REVERT: A 123 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7922 (pttt) REVERT: A 176 VAL cc_start: 0.7917 (t) cc_final: 0.7630 (p) REVERT: A 342 ASP cc_start: 0.7876 (t0) cc_final: 0.7471 (t0) REVERT: A 449 ARG cc_start: 0.6979 (mtm110) cc_final: 0.5816 (ttp-110) REVERT: A 611 ARG cc_start: 0.7306 (ttp-170) cc_final: 0.7029 (tmm160) REVERT: A 652 LYS cc_start: 0.8100 (mmtm) cc_final: 0.7434 (pttm) REVERT: A 697 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7464 (mtmt) REVERT: A 703 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7760 (mt-10) REVERT: A 708 HIS cc_start: 0.7939 (t-170) cc_final: 0.7733 (t70) REVERT: A 763 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8159 (mt) REVERT: A 771 GLU cc_start: 0.7574 (tt0) cc_final: 0.6506 (tt0) REVERT: A 866 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6632 (tpt-90) REVERT: A 876 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7453 (pt0) REVERT: A 1042 PHE cc_start: 0.7663 (m-80) cc_final: 0.7446 (m-80) REVERT: B 123 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7901 (pttt) REVERT: B 176 VAL cc_start: 0.7893 (t) cc_final: 0.7615 (p) REVERT: B 342 ASP cc_start: 0.7838 (t0) cc_final: 0.7435 (t0) REVERT: B 419 LYS cc_start: 0.8415 (tttm) cc_final: 0.8118 (tttp) REVERT: B 449 ARG cc_start: 0.6931 (mtm110) cc_final: 0.5787 (ttp-110) REVERT: B 454 ASP cc_start: 0.7041 (p0) cc_final: 0.6828 (p0) REVERT: B 611 ARG cc_start: 0.7390 (ttp-170) cc_final: 0.6473 (mtp-110) REVERT: B 652 LYS cc_start: 0.8083 (mmtm) cc_final: 0.7413 (pttm) REVERT: B 697 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7469 (mtmt) REVERT: B 703 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7756 (mt-10) REVERT: B 771 GLU cc_start: 0.7732 (tt0) cc_final: 0.6702 (tt0) outliers start: 54 outliers final: 25 residues processed: 241 average time/residue: 1.1698 time to fit residues: 312.5251 Evaluate side-chains 239 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 176 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 480 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 868 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.188763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.147145 restraints weight = 14768.913| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.55 r_work: 0.3468 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14874 Z= 0.152 Angle : 0.562 7.451 20146 Z= 0.287 Chirality : 0.040 0.149 2372 Planarity : 0.004 0.038 2472 Dihedral : 5.101 45.075 2020 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.06 % Allowed : 15.50 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.20), residues: 1836 helix: 1.33 (0.15), residues: 1226 sheet: 1.86 (0.61), residues: 72 loop : -0.91 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 493 HIS 0.005 0.001 HIS B 120 PHE 0.016 0.002 PHE B 636 TYR 0.011 0.001 TYR A 769 ARG 0.006 0.000 ARG B 378 Details of bonding type rmsd hydrogen bonds : bond 0.04167 ( 980) hydrogen bonds : angle 4.72076 ( 2856) covalent geometry : bond 0.00355 (14874) covalent geometry : angle 0.56234 (20146) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 209 time to evaluate : 1.657 Fit side-chains REVERT: A 123 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7931 (ptmt) REVERT: A 176 VAL cc_start: 0.7810 (t) cc_final: 0.7536 (p) REVERT: A 342 ASP cc_start: 0.7929 (t0) cc_final: 0.7424 (t0) REVERT: A 449 ARG cc_start: 0.6952 (mtm110) cc_final: 0.5780 (ttp-110) REVERT: A 555 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8174 (m) REVERT: A 611 ARG cc_start: 0.7435 (ttp-170) cc_final: 0.7190 (tmm160) REVERT: A 652 LYS cc_start: 0.8073 (mmtm) cc_final: 0.7406 (pttm) REVERT: A 697 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7488 (mtmt) REVERT: A 703 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7834 (mt-10) REVERT: A 708 HIS cc_start: 0.7910 (t-170) cc_final: 0.7706 (t70) REVERT: A 763 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8144 (mt) REVERT: A 866 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6569 (tpt-90) REVERT: A 876 GLN cc_start: 0.7620 (pt0) cc_final: 0.7326 (pt0) REVERT: B 123 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7880 (ptmt) REVERT: B 176 VAL cc_start: 0.7815 (t) cc_final: 0.7537 (p) REVERT: B 342 ASP cc_start: 0.7893 (t0) cc_final: 0.7425 (t0) REVERT: B 352 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7603 (mmt-90) REVERT: B 419 LYS cc_start: 0.8394 (tttm) cc_final: 0.8100 (tttp) REVERT: B 449 ARG cc_start: 0.6999 (mtm110) cc_final: 0.5813 (ttp-110) REVERT: B 555 VAL cc_start: 0.8445 (OUTLIER) cc_final: 0.8168 (m) REVERT: B 611 ARG cc_start: 0.7439 (ttp-170) cc_final: 0.6736 (tmm160) REVERT: B 652 LYS cc_start: 0.8025 (mmtm) cc_final: 0.7375 (pttm) REVERT: B 697 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7489 (mtmt) REVERT: B 703 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7853 (mt-10) REVERT: B 708 HIS cc_start: 0.7923 (t-170) cc_final: 0.7706 (t-90) REVERT: B 763 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8139 (mt) REVERT: B 771 GLU cc_start: 0.7734 (tt0) cc_final: 0.6694 (tt0) outliers start: 65 outliers final: 32 residues processed: 244 average time/residue: 1.1245 time to fit residues: 305.9534 Evaluate side-chains 248 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 204 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 866 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 47 optimal weight: 0.0470 chunk 137 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 135 optimal weight: 0.6980 chunk 38 optimal weight: 0.0000 chunk 7 optimal weight: 0.5980 chunk 114 optimal weight: 0.1980 chunk 33 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 chunk 73 optimal weight: 0.1980 overall best weight: 0.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 347 GLN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 347 GLN B 480 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.191752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.149820 restraints weight = 14901.474| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.61 r_work: 0.3529 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14874 Z= 0.114 Angle : 0.526 7.189 20146 Z= 0.268 Chirality : 0.038 0.154 2372 Planarity : 0.004 0.039 2472 Dihedral : 4.790 39.430 2020 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.75 % Allowed : 17.19 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.20), residues: 1836 helix: 1.51 (0.15), residues: 1226 sheet: 1.83 (0.61), residues: 72 loop : -0.92 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 493 HIS 0.004 0.001 HIS A 739 PHE 0.015 0.001 PHE B 353 TYR 0.010 0.001 TYR A 634 ARG 0.004 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 980) hydrogen bonds : angle 4.54734 ( 2856) covalent geometry : bond 0.00250 (14874) covalent geometry : angle 0.52608 (20146) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 224 time to evaluate : 1.673 Fit side-chains REVERT: A 176 VAL cc_start: 0.7704 (OUTLIER) cc_final: 0.7408 (p) REVERT: A 342 ASP cc_start: 0.7830 (t0) cc_final: 0.7349 (t0) REVERT: A 449 ARG cc_start: 0.6808 (mtm110) cc_final: 0.5946 (ttp-110) REVERT: A 555 VAL cc_start: 0.8404 (OUTLIER) cc_final: 0.8160 (m) REVERT: A 611 ARG cc_start: 0.7542 (ttp-170) cc_final: 0.6830 (tmm160) REVERT: A 652 LYS cc_start: 0.8025 (mmtm) cc_final: 0.7382 (pttm) REVERT: A 697 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7457 (mtmt) REVERT: A 703 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7775 (mt-10) REVERT: A 708 HIS cc_start: 0.7979 (t-170) cc_final: 0.7699 (t-90) REVERT: A 763 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8117 (mt) REVERT: A 866 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6515 (tpt-90) REVERT: B 176 VAL cc_start: 0.7683 (OUTLIER) cc_final: 0.7391 (p) REVERT: B 198 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8337 (tp) REVERT: B 342 ASP cc_start: 0.7784 (t0) cc_final: 0.7315 (t0) REVERT: B 352 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7553 (mmt-90) REVERT: B 419 LYS cc_start: 0.8363 (tttm) cc_final: 0.8060 (tttp) REVERT: B 449 ARG cc_start: 0.6821 (mtm110) cc_final: 0.5896 (ttp-110) REVERT: B 555 VAL cc_start: 0.8405 (OUTLIER) cc_final: 0.8136 (m) REVERT: B 611 ARG cc_start: 0.7329 (ttp-170) cc_final: 0.6619 (tmm160) REVERT: B 652 LYS cc_start: 0.7987 (mmtm) cc_final: 0.7341 (pttm) REVERT: B 703 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7831 (mt-10) REVERT: B 708 HIS cc_start: 0.7822 (t-170) cc_final: 0.7604 (t-90) REVERT: B 763 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8144 (mt) REVERT: B 866 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6851 (tpp80) outliers start: 60 outliers final: 29 residues processed: 249 average time/residue: 1.0950 time to fit residues: 303.6786 Evaluate side-chains 242 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 200 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 736 ILE Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 866 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 143 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 178 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 179 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 480 GLN ** B 739 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 = 0.4109 r_free = 0.4109 target = 0.189705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.147543 restraints weight = 14791.817| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.57 r_work: 0.3482 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14874 Z= 0.154 Angle : 0.559 8.631 20146 Z= 0.282 Chirality : 0.040 0.151 2372 Planarity : 0.004 0.039 2472 Dihedral : 4.891 42.999 2020 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.06 % Allowed : 17.81 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.20), residues: 1836 helix: 1.46 (0.15), residues: 1226 sheet: 1.92 (0.62), residues: 72 loop : -0.90 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 493 HIS 0.007 0.001 HIS B 120 PHE 0.014 0.002 PHE B 314 TYR 0.011 0.001 TYR A 769 ARG 0.004 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 980) hydrogen bonds : angle 4.61642 ( 2856) covalent geometry : bond 0.00362 (14874) covalent geometry : angle 0.55867 (20146) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 207 time to evaluate : 1.543 Fit side-chains REVERT: A 95 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7913 (mp0) REVERT: A 342 ASP cc_start: 0.7812 (t0) cc_final: 0.7317 (t0) REVERT: A 449 ARG cc_start: 0.6962 (mtm110) cc_final: 0.5937 (ttp-110) REVERT: A 555 VAL cc_start: 0.8422 (OUTLIER) cc_final: 0.8146 (m) REVERT: A 652 LYS cc_start: 0.8073 (mmtm) cc_final: 0.7408 (pttm) REVERT: A 697 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7463 (mtmt) REVERT: A 703 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7763 (mt-10) REVERT: A 763 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8109 (mt) REVERT: A 866 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.6517 (tpt-90) REVERT: A 1011 MET cc_start: 0.8770 (ttm) cc_final: 0.8503 (mtt) REVERT: B 129 MET cc_start: 0.7642 (mmp) cc_final: 0.7384 (mmp) REVERT: B 342 ASP cc_start: 0.7793 (t0) cc_final: 0.7309 (t0) REVERT: B 352 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7566 (mmt-90) REVERT: B 419 LYS cc_start: 0.8378 (tttm) cc_final: 0.8083 (tttp) REVERT: B 449 ARG cc_start: 0.6942 (mtm110) cc_final: 0.5948 (ttp-110) REVERT: B 555 VAL cc_start: 0.8434 (OUTLIER) cc_final: 0.8158 (m) REVERT: B 652 LYS cc_start: 0.8072 (mmtm) cc_final: 0.7405 (pttm) REVERT: B 697 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7478 (mtmt) REVERT: B 703 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7798 (mt-10) REVERT: B 763 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8137 (mt) REVERT: B 866 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6900 (tpp80) outliers start: 65 outliers final: 36 residues processed: 244 average time/residue: 1.0871 time to fit residues: 295.3520 Evaluate side-chains 247 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 866 ARG Chi-restraints excluded: chain B residue 890 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 27 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 135 optimal weight: 0.6980 chunk 173 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 480 GLN ** B 739 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 = 0.4107 r_free = 0.4107 target = 0.189510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.147150 restraints weight = 14692.178| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.60 r_work: 0.3466 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14874 Z= 0.149 Angle : 0.561 7.934 20146 Z= 0.283 Chirality : 0.040 0.149 2372 Planarity : 0.004 0.040 2472 Dihedral : 4.904 43.787 2020 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.88 % Allowed : 17.94 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.20), residues: 1836 helix: 1.44 (0.15), residues: 1228 sheet: 1.89 (0.62), residues: 72 loop : -0.88 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 493 HIS 0.006 0.001 HIS B 120 PHE 0.016 0.002 PHE A 636 TYR 0.011 0.001 TYR A 769 ARG 0.003 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 980) hydrogen bonds : angle 4.62245 ( 2856) covalent geometry : bond 0.00351 (14874) covalent geometry : angle 0.56083 (20146) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 206 time to evaluate : 1.553 Fit side-chains REVERT: A 95 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7956 (mp0) REVERT: A 342 ASP cc_start: 0.7780 (t0) cc_final: 0.7275 (t0) REVERT: A 419 LYS cc_start: 0.8369 (tttm) cc_final: 0.8064 (tttp) REVERT: A 449 ARG cc_start: 0.7001 (mtm110) cc_final: 0.5951 (ttp-110) REVERT: A 555 VAL cc_start: 0.8432 (OUTLIER) cc_final: 0.8154 (m) REVERT: A 652 LYS cc_start: 0.8061 (mmtm) cc_final: 0.7388 (pttm) REVERT: A 697 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7447 (mtmt) REVERT: A 703 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7761 (mt-10) REVERT: A 763 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8089 (mt) REVERT: A 866 ARG cc_start: 0.7164 (OUTLIER) cc_final: 0.6511 (tpt-90) REVERT: A 907 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6683 (tp) REVERT: A 1011 MET cc_start: 0.8750 (ttm) cc_final: 0.8497 (mtt) REVERT: B 342 ASP cc_start: 0.7777 (t0) cc_final: 0.7281 (t0) REVERT: B 352 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7683 (mmt-90) REVERT: B 419 LYS cc_start: 0.8383 (tttm) cc_final: 0.8092 (tttp) REVERT: B 449 ARG cc_start: 0.7007 (mtm110) cc_final: 0.5959 (ttp-110) REVERT: B 555 VAL cc_start: 0.8430 (OUTLIER) cc_final: 0.8155 (m) REVERT: B 652 LYS cc_start: 0.8066 (mmtm) cc_final: 0.7390 (pttm) REVERT: B 697 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7518 (mtmt) REVERT: B 703 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7787 (mt-10) REVERT: B 763 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8130 (mt) REVERT: B 866 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6867 (tpp80) outliers start: 62 outliers final: 36 residues processed: 242 average time/residue: 1.1050 time to fit residues: 297.9373 Evaluate side-chains 237 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 189 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 866 ARG Chi-restraints excluded: chain B residue 890 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 126 optimal weight: 2.9990 chunk 114 optimal weight: 0.1980 chunk 124 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 140 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 145 optimal weight: 0.3980 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 480 GLN ** B 739 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 = 0.4119 r_free = 0.4119 target = 0.190677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.148547 restraints weight = 14689.208| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.56 r_work: 0.3503 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14874 Z= 0.128 Angle : 0.555 12.119 20146 Z= 0.277 Chirality : 0.039 0.187 2372 Planarity : 0.004 0.040 2472 Dihedral : 4.818 42.544 2020 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.75 % Allowed : 17.94 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.20), residues: 1836 helix: 1.50 (0.15), residues: 1228 sheet: 1.83 (0.61), residues: 72 loop : -0.91 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 493 HIS 0.004 0.001 HIS B 120 PHE 0.016 0.001 PHE A 636 TYR 0.010 0.001 TYR B 634 ARG 0.004 0.000 ARG A 611 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 980) hydrogen bonds : angle 4.56083 ( 2856) covalent geometry : bond 0.00295 (14874) covalent geometry : angle 0.55492 (20146) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 208 time to evaluate : 1.602 Fit side-chains REVERT: A 95 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7945 (mp0) REVERT: A 176 VAL cc_start: 0.7629 (OUTLIER) cc_final: 0.7308 (p) REVERT: A 293 MET cc_start: 0.8899 (mtt) cc_final: 0.8688 (mtt) REVERT: A 342 ASP cc_start: 0.7725 (t0) cc_final: 0.7231 (t0) REVERT: A 555 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.8122 (m) REVERT: A 570 GLN cc_start: 0.7731 (mp10) cc_final: 0.7375 (mt0) REVERT: A 610 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7846 (mp0) REVERT: A 652 LYS cc_start: 0.8097 (mmtm) cc_final: 0.7482 (pttm) REVERT: A 697 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7412 (mtmt) REVERT: A 703 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7730 (mt-10) REVERT: A 763 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8041 (mt) REVERT: A 866 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6676 (tpp80) REVERT: A 907 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6673 (tp) REVERT: B 176 VAL cc_start: 0.7590 (OUTLIER) cc_final: 0.7265 (p) REVERT: B 342 ASP cc_start: 0.7725 (t0) cc_final: 0.7228 (t0) REVERT: B 352 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7552 (mmt-90) REVERT: B 449 ARG cc_start: 0.6960 (mtm110) cc_final: 0.5950 (ttp-110) REVERT: B 555 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.8137 (m) REVERT: B 570 GLN cc_start: 0.7743 (mp10) cc_final: 0.7382 (mt0) REVERT: B 610 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7780 (mp0) REVERT: B 652 LYS cc_start: 0.8041 (mmtm) cc_final: 0.7450 (pttm) REVERT: B 697 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7441 (mtmt) REVERT: B 703 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7758 (mt-10) REVERT: B 763 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8115 (mt) REVERT: B 866 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6829 (tpp80) outliers start: 60 outliers final: 35 residues processed: 243 average time/residue: 1.0638 time to fit residues: 288.7420 Evaluate side-chains 251 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 866 ARG Chi-restraints excluded: chain B residue 890 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 158 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 chunk 182 optimal weight: 0.8980 chunk 173 optimal weight: 0.9980 chunk 170 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 480 GLN ** B 739 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 = 0.4109 r_free = 0.4109 target = 0.189472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.147316 restraints weight = 14696.070| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.57 r_work: 0.3472 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14874 Z= 0.158 Angle : 0.577 11.845 20146 Z= 0.288 Chirality : 0.041 0.155 2372 Planarity : 0.004 0.042 2472 Dihedral : 4.890 44.201 2020 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.50 % Allowed : 18.50 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.20), residues: 1836 helix: 1.43 (0.15), residues: 1228 sheet: 1.91 (0.62), residues: 72 loop : -0.87 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 493 HIS 0.006 0.001 HIS B 120 PHE 0.017 0.002 PHE A 636 TYR 0.011 0.001 TYR B 769 ARG 0.004 0.000 ARG A 611 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 980) hydrogen bonds : angle 4.62393 ( 2856) covalent geometry : bond 0.00378 (14874) covalent geometry : angle 0.57678 (20146) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 197 time to evaluate : 1.667 Fit side-chains REVERT: A 95 GLU cc_start: 0.8245 (mm-30) cc_final: 0.8014 (mp0) REVERT: A 176 VAL cc_start: 0.7668 (OUTLIER) cc_final: 0.7331 (p) REVERT: A 342 ASP cc_start: 0.7705 (t0) cc_final: 0.7202 (t0) REVERT: A 449 ARG cc_start: 0.6819 (mtm-85) cc_final: 0.5774 (ttp-110) REVERT: A 452 ARG cc_start: 0.6975 (mmm160) cc_final: 0.6768 (mmm160) REVERT: A 555 VAL cc_start: 0.8425 (OUTLIER) cc_final: 0.8149 (m) REVERT: A 570 GLN cc_start: 0.7730 (mp10) cc_final: 0.7381 (mt0) REVERT: A 610 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7913 (mp0) REVERT: A 652 LYS cc_start: 0.8102 (mmtm) cc_final: 0.7405 (pttm) REVERT: A 697 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7396 (mtmt) REVERT: A 703 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: A 763 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8144 (mt) REVERT: A 866 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.6740 (tpp80) REVERT: A 907 LEU cc_start: 0.6889 (OUTLIER) cc_final: 0.6664 (tp) REVERT: B 342 ASP cc_start: 0.7718 (t0) cc_final: 0.7224 (t0) REVERT: B 352 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7672 (mmt-90) REVERT: B 419 LYS cc_start: 0.8589 (tttm) cc_final: 0.8322 (tttp) REVERT: B 449 ARG cc_start: 0.7029 (mtm110) cc_final: 0.5936 (ttp-110) REVERT: B 452 ARG cc_start: 0.6984 (mmm160) cc_final: 0.6756 (mmm160) REVERT: B 503 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7992 (mt) REVERT: B 555 VAL cc_start: 0.8443 (OUTLIER) cc_final: 0.8161 (m) REVERT: B 570 GLN cc_start: 0.7748 (mp10) cc_final: 0.7400 (mt0) REVERT: B 610 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7799 (mp0) REVERT: B 652 LYS cc_start: 0.8073 (mmtm) cc_final: 0.7412 (pttm) REVERT: B 697 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7450 (mtmt) REVERT: B 703 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7765 (mt-10) REVERT: B 763 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8136 (mt) REVERT: B 866 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6841 (tpp80) outliers start: 56 outliers final: 37 residues processed: 229 average time/residue: 1.1327 time to fit residues: 288.2704 Evaluate side-chains 246 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 195 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 866 ARG Chi-restraints excluded: chain B residue 890 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 65 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 chunk 132 optimal weight: 0.5980 chunk 177 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 480 GLN ** B 739 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 = 0.4119 r_free = 0.4119 target = 0.190732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.149165 restraints weight = 14884.375| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.52 r_work: 0.3488 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14874 Z= 0.140 Angle : 0.563 11.514 20146 Z= 0.282 Chirality : 0.040 0.151 2372 Planarity : 0.004 0.042 2472 Dihedral : 4.849 43.836 2020 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.69 % Allowed : 18.38 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.20), residues: 1836 helix: 1.46 (0.15), residues: 1228 sheet: 1.94 (0.62), residues: 72 loop : -0.87 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 493 HIS 0.005 0.001 HIS B 120 PHE 0.017 0.001 PHE A 636 TYR 0.013 0.001 TYR A 346 ARG 0.004 0.000 ARG B1035 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 980) hydrogen bonds : angle 4.58964 ( 2856) covalent geometry : bond 0.00330 (14874) covalent geometry : angle 0.56343 (20146) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10845.30 seconds wall clock time: 187 minutes 30.32 seconds (11250.32 seconds total)