Starting phenix.real_space_refine on Sat Aug 23 08:08:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wot_37698/08_2025/8wot_37698_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wot_37698/08_2025/8wot_37698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wot_37698/08_2025/8wot_37698_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wot_37698/08_2025/8wot_37698_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wot_37698/08_2025/8wot_37698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wot_37698/08_2025/8wot_37698.map" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 58 5.16 5 C 7106 2.51 5 N 1644 2.21 5 O 1862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10672 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5139 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 611} Chain breaks: 3 Chain: "B" Number of atoms: 5139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5139 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 611} Chain breaks: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 141 Unusual residues: {' ZN': 1, 'CLR': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 141 Unusual residues: {' ZN': 1, 'CLR': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.68, per 1000 atoms: 0.25 Number of scatterers: 10672 At special positions: 0 Unit cell: (98.716, 86.802, 137.011, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 58 16.00 O 1862 8.00 N 1644 7.00 C 7106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 222 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 222 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 479 " - pdb=" SG CYS B 565 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 901 " - " ASN A 67 " " NAG A 902 " - " ASN A 136 " " NAG B 901 " - " ASN B 67 " " NAG B 902 " - " ASN B 136 " " NAG C 1 " - " ASN A 83 " " NAG D 1 " - " ASN A 57 " " NAG E 1 " - " ASN B 83 " " NAG F 1 " - " ASN B 57 " Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 425.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 907 " pdb="ZN ZN A 907 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 907 " - pdb=" NE2 HIS A 796 " pdb="ZN ZN A 907 " - pdb=" NE2 HIS A 800 " pdb=" ZN B 907 " pdb="ZN ZN B 907 " - pdb=" NE2 HIS B 563 " pdb="ZN ZN B 907 " - pdb=" NE2 HIS B 800 " pdb="ZN ZN B 907 " - pdb=" NE2 HIS B 796 " 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 49.8% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 302 through 336 removed outlier: 3.871A pdb=" N TYR A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 474 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 482 through 486 removed outlier: 3.989A pdb=" N ALA A 486 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 500 removed outlier: 3.925A pdb=" N ILE A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 529 removed outlier: 3.927A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY A 508 " --> pdb=" O HIS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 536 removed outlier: 3.607A pdb=" N GLU A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 565 removed outlier: 3.557A pdb=" N TYR A 546 " --> pdb=" O PHE A 542 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N CYS A 565 " --> pdb=" O CYS A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.928A pdb=" N PHE A 571 " --> pdb=" O TYR A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 594 removed outlier: 3.812A pdb=" N TYR A 579 " --> pdb=" O THR A 575 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 622 removed outlier: 3.898A pdb=" N TYR A 605 " --> pdb=" O ALA A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 649 Processing helix chain 'A' and resid 689 through 709 Processing helix chain 'A' and resid 713 through 740 Processing helix chain 'A' and resid 745 through 768 removed outlier: 3.700A pdb=" N GLN A 768 " --> pdb=" O TYR A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 794 through 817 Processing helix chain 'B' and resid 38 through 43 removed outlier: 3.517A pdb=" N ALA B 42 " --> pdb=" O ASP B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 336 removed outlier: 3.866A pdb=" N TYR B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N PHE B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 474 removed outlier: 3.549A pdb=" N VAL B 453 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 482 through 486 removed outlier: 3.997A pdb=" N ALA B 486 " --> pdb=" O PHE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'B' and resid 501 through 529 removed outlier: 3.879A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY B 508 " --> pdb=" O HIS B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 536 removed outlier: 3.563A pdb=" N GLU B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 565 removed outlier: 3.782A pdb=" N VAL B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N CYS B 565 " --> pdb=" O CYS B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 571 removed outlier: 4.086A pdb=" N PHE B 571 " --> pdb=" O TYR B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 594 removed outlier: 3.853A pdb=" N MET B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG B 593 " --> pdb=" O LEU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 622 removed outlier: 3.773A pdb=" N TYR B 605 " --> pdb=" O ALA B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 649 Processing helix chain 'B' and resid 689 through 709 Processing helix chain 'B' and resid 713 through 740 Processing helix chain 'B' and resid 745 through 768 removed outlier: 3.647A pdb=" N GLN B 768 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 794 through 817 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 70 Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 114 Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 171 removed outlier: 4.753A pdb=" N LYS A 192 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 178 through 181 Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 56 Processing sheet with id=AA7, first strand: chain 'B' and resid 62 through 70 Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AA9, first strand: chain 'B' and resid 170 through 171 removed outlier: 4.765A pdb=" N LYS B 192 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 181 612 hydrogen bonds defined for protein. 1758 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3170 1.34 - 1.46: 2831 1.46 - 1.58: 4885 1.58 - 1.70: 0 1.70 - 1.81: 90 Bond restraints: 10976 Sorted by residual: bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.64e+00 bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.59e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.86e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.73e+00 ... (remaining 10971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 14892 2.62 - 5.25: 83 5.25 - 7.87: 3 7.87 - 10.50: 0 10.50 - 13.12: 2 Bond angle restraints: 14980 Sorted by residual: angle pdb=" C SER A 600 " pdb=" CA SER A 600 " pdb=" CB SER A 600 " ideal model delta sigma weight residual 116.54 110.44 6.10 1.15e+00 7.56e-01 2.81e+01 angle pdb=" C SER B 600 " pdb=" CA SER B 600 " pdb=" CB SER B 600 " ideal model delta sigma weight residual 116.54 110.48 6.06 1.15e+00 7.56e-01 2.78e+01 angle pdb=" CA LEU B 789 " pdb=" CB LEU B 789 " pdb=" CG LEU B 789 " ideal model delta sigma weight residual 116.30 129.42 -13.12 3.50e+00 8.16e-02 1.41e+01 angle pdb=" CA SER A 600 " pdb=" C SER A 600 " pdb=" N ALA A 601 " ideal model delta sigma weight residual 119.52 116.57 2.95 7.90e-01 1.60e+00 1.39e+01 angle pdb=" CA SER B 600 " pdb=" C SER B 600 " pdb=" N ALA B 601 " ideal model delta sigma weight residual 119.52 116.63 2.89 7.90e-01 1.60e+00 1.33e+01 ... (remaining 14975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.66: 6356 25.66 - 51.33: 481 51.33 - 76.99: 59 76.99 - 102.66: 22 102.66 - 128.32: 10 Dihedral angle restraints: 6928 sinusoidal: 3148 harmonic: 3780 Sorted by residual: dihedral pdb=" C2 NAG A 901 " pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " pdb=" C5 NAG A 901 " ideal model delta sinusoidal sigma weight residual -62.96 65.36 -128.32 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C2 NAG B 901 " pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " pdb=" C5 NAG B 901 " ideal model delta sinusoidal sigma weight residual -62.96 65.32 -128.28 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C2 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" C4 NAG F 1 " pdb=" O4 NAG F 1 " ideal model delta sinusoidal sigma weight residual 175.11 62.53 112.58 1 3.00e+01 1.11e-03 1.48e+01 ... (remaining 6925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1596 0.069 - 0.138: 151 0.138 - 0.207: 3 0.207 - 0.276: 0 0.276 - 0.345: 2 Chirality restraints: 1752 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 57 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 57 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 67 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.71e-01 ... (remaining 1749 not shown) Planarity restraints: 1810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 83 " 0.002 2.00e-02 2.50e+03 1.90e-02 4.50e+00 pdb=" CG ASN B 83 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN B 83 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN B 83 " 0.027 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 747 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO B 748 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 748 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 748 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 747 " -0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO A 748 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 748 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 748 " -0.023 5.00e-02 4.00e+02 ... (remaining 1807 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 113 2.60 - 3.17: 9668 3.17 - 3.75: 15866 3.75 - 4.32: 20935 4.32 - 4.90: 35956 Nonbonded interactions: 82538 Sorted by model distance: nonbonded pdb=" OG SER B 701 " pdb=" OH TYR B 717 " model vdw 2.020 3.040 nonbonded pdb=" OH TYR B 64 " pdb=" OH TYR B 159 " model vdw 2.073 3.040 nonbonded pdb=" OG SER A 740 " pdb=" OE2 GLU A 742 " model vdw 2.097 3.040 nonbonded pdb=" OH TYR A 64 " pdb=" OH TYR A 159 " model vdw 2.103 3.040 nonbonded pdb=" N GLU B 137 " pdb=" OE1 GLU B 137 " model vdw 2.121 3.120 ... (remaining 82533 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 4.310 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.330 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11000 Z= 0.148 Angle : 0.552 13.124 15028 Z= 0.280 Chirality : 0.040 0.345 1752 Planarity : 0.003 0.045 1802 Dihedral : 17.953 128.319 4470 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 30.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.27 % Allowed : 29.86 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.25), residues: 1256 helix: 3.00 (0.21), residues: 580 sheet: 0.62 (0.33), residues: 268 loop : -2.36 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 37 TYR 0.016 0.001 TYR B 709 PHE 0.025 0.001 PHE B 705 TRP 0.013 0.001 TRP A 446 HIS 0.001 0.000 HIS B 636 Details of bonding type rmsd covalent geometry : bond 0.00303 (10976) covalent geometry : angle 0.51892 (14980) SS BOND : bond 0.00102 ( 6) SS BOND : angle 0.41807 ( 12) hydrogen bonds : bond 0.09038 ( 612) hydrogen bonds : angle 4.77355 ( 1758) metal coordination : bond 0.00164 ( 6) link_BETA1-4 : bond 0.00181 ( 4) link_BETA1-4 : angle 1.61689 ( 12) link_NAG-ASN : bond 0.00516 ( 8) link_NAG-ASN : angle 4.60749 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 129 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 689 MET cc_start: 0.8366 (pmm) cc_final: 0.7892 (pmm) outliers start: 3 outliers final: 2 residues processed: 130 average time/residue: 0.0841 time to fit residues: 16.8676 Evaluate side-chains 131 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain B residue 714 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN B 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.141864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.096034 restraints weight = 17366.174| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.84 r_work: 0.3296 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 11000 Z= 0.281 Angle : 0.782 13.867 15028 Z= 0.376 Chirality : 0.052 0.569 1752 Planarity : 0.005 0.049 1802 Dihedral : 12.791 111.061 2158 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.72 % Favored : 92.12 % Rotamer: Outliers : 4.42 % Allowed : 25.09 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.24), residues: 1256 helix: 1.87 (0.21), residues: 586 sheet: 0.25 (0.31), residues: 280 loop : -2.64 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 781 TYR 0.035 0.002 TYR A 717 PHE 0.024 0.002 PHE A 705 TRP 0.013 0.002 TRP A 106 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00674 (10976) covalent geometry : angle 0.72395 (14980) SS BOND : bond 0.00190 ( 6) SS BOND : angle 0.98497 ( 12) hydrogen bonds : bond 0.05294 ( 612) hydrogen bonds : angle 4.69156 ( 1758) metal coordination : bond 0.00609 ( 6) link_BETA1-4 : bond 0.00452 ( 4) link_BETA1-4 : angle 2.64444 ( 12) link_NAG-ASN : bond 0.00809 ( 8) link_NAG-ASN : angle 7.17347 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 137 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 287 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7004 (tt) REVERT: A 520 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8401 (tp) REVERT: A 540 LYS cc_start: 0.6352 (tmtt) cc_final: 0.5941 (tmtt) REVERT: A 586 MET cc_start: 0.8162 (mmp) cc_final: 0.7956 (mmp) outliers start: 50 outliers final: 28 residues processed: 173 average time/residue: 0.0752 time to fit residues: 20.3711 Evaluate side-chains 155 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 628 PHE Chi-restraints excluded: chain B residue 750 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 35 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 28 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 796 HIS B 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.143937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.098167 restraints weight = 16954.578| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.92 r_work: 0.3339 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.879 11000 Z= 0.311 Angle : 0.687 13.139 15028 Z= 0.322 Chirality : 0.047 0.554 1752 Planarity : 0.004 0.049 1802 Dihedral : 12.045 109.405 2154 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.25 % Favored : 94.59 % Rotamer: Outliers : 2.74 % Allowed : 26.68 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.24), residues: 1256 helix: 1.83 (0.21), residues: 590 sheet: 0.60 (0.32), residues: 272 loop : -2.49 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 781 TYR 0.036 0.002 TYR A 717 PHE 0.027 0.001 PHE B 705 TRP 0.013 0.001 TRP A 446 HIS 0.003 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00300 (10976) covalent geometry : angle 0.62419 (14980) SS BOND : bond 0.00190 ( 6) SS BOND : angle 0.60406 ( 12) hydrogen bonds : bond 0.04501 ( 612) hydrogen bonds : angle 4.44753 ( 1758) metal coordination : bond 0.35884 ( 6) link_BETA1-4 : bond 0.00495 ( 4) link_BETA1-4 : angle 2.93781 ( 12) link_NAG-ASN : bond 0.00898 ( 8) link_NAG-ASN : angle 6.90745 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 287 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6872 (tt) REVERT: A 520 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8425 (tp) REVERT: A 540 LYS cc_start: 0.6222 (tmtt) cc_final: 0.5674 (tmtt) REVERT: A 613 MET cc_start: 0.8581 (mmm) cc_final: 0.8240 (mmm) outliers start: 31 outliers final: 20 residues processed: 158 average time/residue: 0.0799 time to fit residues: 19.3105 Evaluate side-chains 153 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 628 PHE Chi-restraints excluded: chain B residue 750 PHE Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.144315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.098453 restraints weight = 17040.962| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.94 r_work: 0.3353 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11000 Z= 0.142 Angle : 0.683 13.492 15028 Z= 0.319 Chirality : 0.047 0.551 1752 Planarity : 0.004 0.050 1802 Dihedral : 11.528 108.619 2154 Min Nonbonded Distance : 1.616 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.61 % Favored : 93.23 % Rotamer: Outliers : 3.62 % Allowed : 26.33 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.24), residues: 1256 helix: 1.81 (0.21), residues: 590 sheet: 0.70 (0.32), residues: 268 loop : -2.54 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 712 TYR 0.034 0.001 TYR A 717 PHE 0.020 0.001 PHE A 573 TRP 0.016 0.001 TRP A 629 HIS 0.009 0.001 HIS A 800 Details of bonding type rmsd covalent geometry : bond 0.00323 (10976) covalent geometry : angle 0.61856 (14980) SS BOND : bond 0.00175 ( 6) SS BOND : angle 0.63332 ( 12) hydrogen bonds : bond 0.04361 ( 612) hydrogen bonds : angle 4.32931 ( 1758) metal coordination : bond 0.00681 ( 6) link_BETA1-4 : bond 0.00553 ( 4) link_BETA1-4 : angle 3.04678 ( 12) link_NAG-ASN : bond 0.00908 ( 8) link_NAG-ASN : angle 6.98630 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 287 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6834 (tt) REVERT: A 520 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8447 (tp) REVERT: A 540 LYS cc_start: 0.6241 (tmtt) cc_final: 0.5653 (tmtt) REVERT: B 686 MET cc_start: 0.5662 (pmm) cc_final: 0.5185 (pmm) outliers start: 41 outliers final: 27 residues processed: 165 average time/residue: 0.0772 time to fit residues: 19.5563 Evaluate side-chains 160 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 628 PHE Chi-restraints excluded: chain B residue 750 PHE Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 122 optimal weight: 4.9990 chunk 107 optimal weight: 0.0370 chunk 37 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 84 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.144826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.098928 restraints weight = 16769.047| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.91 r_work: 0.3349 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11000 Z= 0.137 Angle : 0.686 13.647 15028 Z= 0.316 Chirality : 0.047 0.546 1752 Planarity : 0.004 0.049 1802 Dihedral : 11.155 108.156 2154 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.65 % Favored : 94.19 % Rotamer: Outliers : 3.98 % Allowed : 26.41 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.24), residues: 1256 helix: 1.79 (0.21), residues: 592 sheet: 0.75 (0.32), residues: 268 loop : -2.56 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 712 TYR 0.030 0.001 TYR A 717 PHE 0.030 0.001 PHE A 705 TRP 0.023 0.002 TRP B 446 HIS 0.003 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00311 (10976) covalent geometry : angle 0.62103 (14980) SS BOND : bond 0.00174 ( 6) SS BOND : angle 0.58476 ( 12) hydrogen bonds : bond 0.04235 ( 612) hydrogen bonds : angle 4.26253 ( 1758) metal coordination : bond 0.00604 ( 6) link_BETA1-4 : bond 0.00478 ( 4) link_BETA1-4 : angle 3.13345 ( 12) link_NAG-ASN : bond 0.00945 ( 8) link_NAG-ASN : angle 6.97329 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 143 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 287 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6868 (tt) REVERT: A 520 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8472 (tp) REVERT: A 540 LYS cc_start: 0.6270 (tmtt) cc_final: 0.5538 (tmtt) REVERT: A 580 MET cc_start: 0.8069 (tpp) cc_final: 0.7757 (tpp) REVERT: A 584 LEU cc_start: 0.9246 (mt) cc_final: 0.9045 (mp) outliers start: 45 outliers final: 35 residues processed: 176 average time/residue: 0.0784 time to fit residues: 20.7898 Evaluate side-chains 166 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 628 PHE Chi-restraints excluded: chain B residue 714 PHE Chi-restraints excluded: chain B residue 750 PHE Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 27 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 58 optimal weight: 0.0170 chunk 42 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 796 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.145351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.099570 restraints weight = 16923.163| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.92 r_work: 0.3352 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.878 11000 Z= 0.309 Angle : 0.692 13.728 15028 Z= 0.317 Chirality : 0.047 0.541 1752 Planarity : 0.004 0.049 1802 Dihedral : 10.849 107.801 2154 Min Nonbonded Distance : 1.646 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.05 % Favored : 93.79 % Rotamer: Outliers : 3.45 % Allowed : 26.94 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.24), residues: 1256 helix: 1.88 (0.21), residues: 582 sheet: 0.78 (0.32), residues: 268 loop : -2.58 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 712 TYR 0.040 0.001 TYR A 717 PHE 0.031 0.001 PHE B 705 TRP 0.023 0.001 TRP B 446 HIS 0.003 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00301 (10976) covalent geometry : angle 0.62826 (14980) SS BOND : bond 0.00168 ( 6) SS BOND : angle 0.56504 ( 12) hydrogen bonds : bond 0.04131 ( 612) hydrogen bonds : angle 4.22257 ( 1758) metal coordination : bond 0.35848 ( 6) link_BETA1-4 : bond 0.00465 ( 4) link_BETA1-4 : angle 3.21269 ( 12) link_NAG-ASN : bond 0.00956 ( 8) link_NAG-ASN : angle 6.96299 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 287 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6843 (tt) REVERT: A 520 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8474 (tp) REVERT: A 580 MET cc_start: 0.8069 (tpp) cc_final: 0.7762 (tpp) REVERT: B 686 MET cc_start: 0.5735 (pmm) cc_final: 0.4854 (pmm) outliers start: 39 outliers final: 33 residues processed: 169 average time/residue: 0.0834 time to fit residues: 21.7842 Evaluate side-chains 168 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 628 PHE Chi-restraints excluded: chain B residue 750 PHE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 788 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 87 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.142372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.098212 restraints weight = 16852.774| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 3.63 r_work: 0.3258 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 11000 Z= 0.248 Angle : 0.773 14.320 15028 Z= 0.363 Chirality : 0.050 0.566 1752 Planarity : 0.004 0.048 1802 Dihedral : 10.777 107.944 2154 Min Nonbonded Distance : 1.663 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.37 % Favored : 93.47 % Rotamer: Outliers : 4.59 % Allowed : 26.50 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.24), residues: 1256 helix: 1.63 (0.21), residues: 586 sheet: 0.55 (0.32), residues: 268 loop : -2.58 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 712 TYR 0.032 0.002 TYR A 717 PHE 0.033 0.002 PHE A 705 TRP 0.014 0.002 TRP B 446 HIS 0.008 0.001 HIS B 800 Details of bonding type rmsd covalent geometry : bond 0.00590 (10976) covalent geometry : angle 0.70982 (14980) SS BOND : bond 0.00180 ( 6) SS BOND : angle 0.77810 ( 12) hydrogen bonds : bond 0.04991 ( 612) hydrogen bonds : angle 4.39783 ( 1758) metal coordination : bond 0.01423 ( 6) link_BETA1-4 : bond 0.00572 ( 4) link_BETA1-4 : angle 3.21818 ( 12) link_NAG-ASN : bond 0.00850 ( 8) link_NAG-ASN : angle 7.36622 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 137 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 287 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.6922 (tt) REVERT: A 520 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8539 (tp) REVERT: A 540 LYS cc_start: 0.6293 (tmtt) cc_final: 0.6004 (tmtt) REVERT: B 540 LYS cc_start: 0.6080 (tmtt) cc_final: 0.5799 (tptp) outliers start: 52 outliers final: 38 residues processed: 176 average time/residue: 0.0870 time to fit residues: 23.5030 Evaluate side-chains 170 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 629 TRP Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 750 PHE Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 102 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 81 optimal weight: 0.1980 chunk 40 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.145111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.101022 restraints weight = 16647.631| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.64 r_work: 0.3309 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11000 Z= 0.129 Angle : 0.716 13.898 15028 Z= 0.327 Chirality : 0.047 0.538 1752 Planarity : 0.004 0.047 1802 Dihedral : 10.544 107.723 2154 Min Nonbonded Distance : 1.634 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.18 % Favored : 94.67 % Rotamer: Outliers : 3.36 % Allowed : 27.65 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.24), residues: 1256 helix: 1.78 (0.21), residues: 576 sheet: 0.73 (0.32), residues: 268 loop : -2.55 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 712 TYR 0.039 0.001 TYR A 717 PHE 0.040 0.001 PHE A 705 TRP 0.017 0.001 TRP A 446 HIS 0.003 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00286 (10976) covalent geometry : angle 0.65214 (14980) SS BOND : bond 0.00173 ( 6) SS BOND : angle 0.55597 ( 12) hydrogen bonds : bond 0.04223 ( 612) hydrogen bonds : angle 4.22469 ( 1758) metal coordination : bond 0.00599 ( 6) link_BETA1-4 : bond 0.00399 ( 4) link_BETA1-4 : angle 3.29033 ( 12) link_NAG-ASN : bond 0.00982 ( 8) link_NAG-ASN : angle 7.04012 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 287 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6839 (tt) REVERT: A 520 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8522 (tp) REVERT: A 540 LYS cc_start: 0.6229 (tmtt) cc_final: 0.5748 (tmtt) REVERT: B 540 LYS cc_start: 0.6037 (tmtt) cc_final: 0.5813 (tptp) REVERT: B 686 MET cc_start: 0.5737 (pmm) cc_final: 0.4833 (pmm) outliers start: 38 outliers final: 30 residues processed: 163 average time/residue: 0.0770 time to fit residues: 19.2483 Evaluate side-chains 163 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 628 PHE Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 14 optimal weight: 0.0970 chunk 81 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.145734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.101876 restraints weight = 16677.735| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 3.63 r_work: 0.3324 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11000 Z= 0.126 Angle : 0.718 13.849 15028 Z= 0.326 Chirality : 0.047 0.540 1752 Planarity : 0.004 0.045 1802 Dihedral : 10.296 107.117 2154 Min Nonbonded Distance : 1.668 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.25 % Favored : 94.59 % Rotamer: Outliers : 3.00 % Allowed : 28.36 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.24), residues: 1256 helix: 1.80 (0.21), residues: 578 sheet: 0.86 (0.32), residues: 268 loop : -2.48 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 712 TYR 0.037 0.001 TYR A 717 PHE 0.029 0.001 PHE A 573 TRP 0.020 0.001 TRP A 446 HIS 0.004 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00281 (10976) covalent geometry : angle 0.65508 (14980) SS BOND : bond 0.00160 ( 6) SS BOND : angle 0.54363 ( 12) hydrogen bonds : bond 0.04056 ( 612) hydrogen bonds : angle 4.18939 ( 1758) metal coordination : bond 0.00395 ( 6) link_BETA1-4 : bond 0.00348 ( 4) link_BETA1-4 : angle 3.35992 ( 12) link_NAG-ASN : bond 0.00998 ( 8) link_NAG-ASN : angle 7.00234 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 89 LEU cc_start: 0.8491 (pt) cc_final: 0.8061 (tt) REVERT: A 287 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.6835 (tt) REVERT: A 326 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.7946 (mt) REVERT: A 520 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8544 (tp) REVERT: A 540 LYS cc_start: 0.6262 (tmtt) cc_final: 0.5775 (tmtt) REVERT: B 540 LYS cc_start: 0.6023 (tmtt) cc_final: 0.5811 (tptp) outliers start: 34 outliers final: 26 residues processed: 159 average time/residue: 0.0751 time to fit residues: 18.4954 Evaluate side-chains 158 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 629 TRP Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 121 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.142807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.098740 restraints weight = 16754.010| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.65 r_work: 0.3267 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11000 Z= 0.222 Angle : 0.776 14.457 15028 Z= 0.361 Chirality : 0.050 0.575 1752 Planarity : 0.004 0.045 1802 Dihedral : 10.321 107.015 2154 Min Nonbonded Distance : 1.663 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.13 % Favored : 93.71 % Rotamer: Outliers : 2.92 % Allowed : 28.45 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.24), residues: 1256 helix: 1.67 (0.21), residues: 576 sheet: 0.65 (0.32), residues: 268 loop : -2.59 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 712 TYR 0.038 0.002 TYR A 717 PHE 0.045 0.002 PHE B 705 TRP 0.015 0.002 TRP A 446 HIS 0.003 0.001 HIS B 563 Details of bonding type rmsd covalent geometry : bond 0.00527 (10976) covalent geometry : angle 0.71337 (14980) SS BOND : bond 0.00198 ( 6) SS BOND : angle 0.72140 ( 12) hydrogen bonds : bond 0.04827 ( 612) hydrogen bonds : angle 4.32906 ( 1758) metal coordination : bond 0.01027 ( 6) link_BETA1-4 : bond 0.00462 ( 4) link_BETA1-4 : angle 3.36032 ( 12) link_NAG-ASN : bond 0.00865 ( 8) link_NAG-ASN : angle 7.33982 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 89 LEU cc_start: 0.8522 (pt) cc_final: 0.8085 (tt) REVERT: A 287 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.6939 (tt) REVERT: A 520 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8596 (tp) REVERT: A 530 ASP cc_start: 0.4222 (OUTLIER) cc_final: 0.3859 (t0) REVERT: A 540 LYS cc_start: 0.6323 (tmtt) cc_final: 0.5888 (tmtt) REVERT: B 540 LYS cc_start: 0.6161 (tmtt) cc_final: 0.5876 (tptp) REVERT: B 686 MET cc_start: 0.5723 (pmm) cc_final: 0.4770 (pmm) outliers start: 33 outliers final: 30 residues processed: 156 average time/residue: 0.0832 time to fit residues: 19.7855 Evaluate side-chains 158 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 628 PHE Chi-restraints excluded: chain B residue 629 TRP Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 41 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 77 optimal weight: 0.0370 chunk 101 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.145185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.101802 restraints weight = 16784.502| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.72 r_work: 0.3315 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11000 Z= 0.132 Angle : 0.727 13.980 15028 Z= 0.331 Chirality : 0.047 0.549 1752 Planarity : 0.004 0.044 1802 Dihedral : 10.194 106.628 2154 Min Nonbonded Distance : 1.640 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.94 % Favored : 94.90 % Rotamer: Outliers : 2.47 % Allowed : 28.98 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.24), residues: 1256 helix: 1.78 (0.21), residues: 574 sheet: 0.79 (0.32), residues: 268 loop : -2.43 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 712 TYR 0.035 0.001 TYR A 717 PHE 0.047 0.001 PHE B 705 TRP 0.019 0.001 TRP A 446 HIS 0.003 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00298 (10976) covalent geometry : angle 0.66301 (14980) SS BOND : bond 0.00210 ( 6) SS BOND : angle 0.52120 ( 12) hydrogen bonds : bond 0.04185 ( 612) hydrogen bonds : angle 4.22050 ( 1758) metal coordination : bond 0.00424 ( 6) link_BETA1-4 : bond 0.00294 ( 4) link_BETA1-4 : angle 3.39735 ( 12) link_NAG-ASN : bond 0.00984 ( 8) link_NAG-ASN : angle 7.08860 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2374.80 seconds wall clock time: 41 minutes 35.81 seconds (2495.81 seconds total)