Starting phenix.real_space_refine on Sun Dec 29 00:09:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qo9_14087/12_2024/7qo9_14087.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qo9_14087/12_2024/7qo9_14087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qo9_14087/12_2024/7qo9_14087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qo9_14087/12_2024/7qo9_14087.map" model { file = "/net/cci-nas-00/data/ceres_data/7qo9_14087/12_2024/7qo9_14087.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qo9_14087/12_2024/7qo9_14087.cif" } resolution = 3.88 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= 0.000 sd= 0.012 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 45 5.16 5 C 5830 2.51 5 N 1523 2.21 5 O 1782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9180 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4568 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 25, 'TRANS': 562} Chain breaks: 14 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 4486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4486 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 26, 'TRANS': 551} Chain breaks: 6 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 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: "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: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 31 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2, 'water': 3} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.45, per 1000 atoms: 0.70 Number of scatterers: 9180 At special positions: 0 Unit cell: (87.5022, 112.046, 122.717, 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 45 16.00 O 1782 8.00 N 1523 7.00 C 5830 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A 837 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.04 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.04 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B 837 " - pdb=" SG CYS B 848 " 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 D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1301 " - " ASN A 231 " " NAG A1302 " - " ASN A 279 " " NAG C 1 " - " ASN A 160 " " NAG D 1 " - " ASN A 120 " " NAG E 1 " - " ASN A 135 " Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.1 seconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2188 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 17 sheets defined 26.2% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 734 through 740 removed outlier: 3.661A pdb=" N TYR A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.500A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 780 Processing helix chain 'A' and resid 846 through 852 removed outlier: 3.589A pdb=" N PHE A 852 " --> pdb=" O CYS A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 874 Processing helix chain 'A' and resid 943 through 962 removed outlier: 4.873A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1022 removed outlier: 4.599A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 368 removed outlier: 3.769A pdb=" N TYR B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 387 removed outlier: 3.762A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 387 " --> pdb=" O LEU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 734 through 739 Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 757 through 779 removed outlier: 3.565A pdb=" N ILE B 767 " --> pdb=" O ALA B 763 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 773 " --> pdb=" O VAL B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 825 through 827 No H-bonds generated for 'chain 'B' and resid 825 through 827' Processing helix chain 'B' and resid 863 through 864 No H-bonds generated for 'chain 'B' and resid 863 through 864' Processing helix chain 'B' and resid 866 through 868 No H-bonds generated for 'chain 'B' and resid 866 through 868' Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.739A pdb=" N GLN B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 980 Processing helix chain 'B' and resid 982 through 1022 removed outlier: 4.466A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.205A pdb=" N VAL A 36 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N SER A 200 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 4.508A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 68 Processing sheet with id=AA5, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA6, first strand: chain 'A' and resid 104 through 105 removed outlier: 3.861A pdb=" N SER A 114 " --> pdb=" O CYS A 129 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS A 129 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE A 126 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE A 163 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL A 128 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N CYS A 161 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N SER A 157 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.626A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER A 313 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 651 through 657 removed outlier: 6.058A pdb=" N THR A 693 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASN A 655 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 724 through 725 Processing sheet with id=AB1, first strand: chain 'A' and resid 732 through 733 Processing sheet with id=AB2, first strand: chain 'B' and resid 308 through 316 removed outlier: 3.807A pdb=" N THR B 312 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 322 through 323 removed outlier: 3.500A pdb=" N ASN B 539 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE B 540 " --> pdb=" O LEU B 543 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 352 through 355 removed outlier: 3.836A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.547A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 430 through 434 removed outlier: 3.708A pdb=" N ARG B 506 " --> pdb=" O TRP B 433 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.593A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 732 through 733 300 hydrogen bonds defined for protein. 819 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: 3.20 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1899 1.33 - 1.45: 2235 1.45 - 1.58: 5160 1.58 - 1.70: 0 1.70 - 1.82: 55 Bond restraints: 9349 Sorted by residual: bond pdb=" N GLN A 625 " pdb=" CA GLN A 625 " ideal model delta sigma weight residual 1.457 1.504 -0.047 1.29e-02 6.01e+03 1.31e+01 bond pdb=" CA SER B 491 " pdb=" CB SER B 491 " ideal model delta sigma weight residual 1.530 1.480 0.050 1.39e-02 5.18e+03 1.30e+01 bond pdb=" N VAL B 480 " pdb=" CA VAL B 480 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.25e-02 6.40e+03 1.29e+01 bond pdb=" N ASP A 624 " pdb=" CA ASP A 624 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.20e-02 6.94e+03 9.24e+00 bond pdb=" N CYS B 485 " pdb=" CA CYS B 485 " ideal model delta sigma weight residual 1.462 1.497 -0.035 1.26e-02 6.30e+03 7.82e+00 ... (remaining 9344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 12443 2.37 - 4.74: 203 4.74 - 7.10: 37 7.10 - 9.47: 3 9.47 - 11.84: 4 Bond angle restraints: 12690 Sorted by residual: angle pdb=" N PRO A 628 " pdb=" CA PRO A 628 " pdb=" CB PRO A 628 " ideal model delta sigma weight residual 103.25 92.75 10.50 1.05e+00 9.07e-01 1.00e+02 angle pdb=" C TYR B 448 " pdb=" CA TYR B 448 " pdb=" CB TYR B 448 " ideal model delta sigma weight residual 110.88 99.97 10.91 1.57e+00 4.06e-01 4.83e+01 angle pdb=" C TYR B 486 " pdb=" CA TYR B 486 " pdb=" CB TYR B 486 " ideal model delta sigma weight residual 109.83 97.99 11.84 1.75e+00 3.27e-01 4.58e+01 angle pdb=" C TYR B 446 " pdb=" CA TYR B 446 " pdb=" CB TYR B 446 " ideal model delta sigma weight residual 114.87 104.90 9.97 1.51e+00 4.39e-01 4.36e+01 angle pdb=" CA ASP A 624 " pdb=" C ASP A 624 " pdb=" O ASP A 624 " ideal model delta sigma weight residual 121.31 116.01 5.30 1.07e+00 8.73e-01 2.45e+01 ... (remaining 12685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.74: 5320 23.74 - 47.48: 327 47.48 - 71.21: 45 71.21 - 94.95: 24 94.95 - 118.69: 13 Dihedral angle restraints: 5729 sinusoidal: 2346 harmonic: 3383 Sorted by residual: dihedral pdb=" CB CYS A 288 " pdb=" SG CYS A 288 " pdb=" SG CYS A 298 " pdb=" CB CYS A 298 " ideal model delta sinusoidal sigma weight residual -86.00 -167.55 81.55 1 1.00e+01 1.00e-02 8.19e+01 dihedral pdb=" CB CYS B 535 " pdb=" SG CYS B 535 " pdb=" SG CYS B 587 " pdb=" CB CYS B 587 " ideal model delta sinusoidal sigma weight residual -86.00 -5.51 -80.49 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CB CYS A 659 " pdb=" SG CYS A 659 " pdb=" SG CYS A 668 " pdb=" CB CYS A 668 " ideal model delta sinusoidal sigma weight residual -86.00 -11.72 -74.28 1 1.00e+01 1.00e-02 7.00e+01 ... (remaining 5726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1436 0.110 - 0.219: 48 0.219 - 0.329: 8 0.329 - 0.438: 3 0.438 - 0.548: 3 Chirality restraints: 1498 Sorted by residual: chirality pdb=" CA TYR B 448 " pdb=" N TYR B 448 " pdb=" C TYR B 448 " pdb=" CB TYR B 448 " both_signs ideal model delta sigma weight residual False 2.51 3.06 -0.55 2.00e-01 2.50e+01 7.50e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 160 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" CA TYR B 446 " pdb=" N TYR B 446 " pdb=" C TYR B 446 " pdb=" CB TYR B 446 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 4.96e+00 ... (remaining 1495 not shown) Planarity restraints: 1620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 627 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.99e+00 pdb=" C THR A 627 " -0.055 2.00e-02 2.50e+03 pdb=" O THR A 627 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO A 628 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 226 " 0.043 5.00e-02 4.00e+02 6.61e-02 6.98e+00 pdb=" N PRO A 227 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 227 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 227 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 79 " 0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO A 80 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 80 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 80 " 0.035 5.00e-02 4.00e+02 ... (remaining 1617 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 528 2.72 - 3.27: 9666 3.27 - 3.81: 14147 3.81 - 4.36: 16230 4.36 - 4.90: 27275 Nonbonded interactions: 67846 Sorted by model distance: nonbonded pdb=" OH TYR A 89 " pdb=" OE1 GLU A 186 " model vdw 2.179 3.040 nonbonded pdb=" O THR B 863 " pdb=" N MET B 866 " model vdw 2.201 3.120 nonbonded pdb=" O VAL A 619 " pdb=" ND1 HIS A 622 " model vdw 2.232 3.120 nonbonded pdb=" OG SER A 110 " pdb=" OE1 GLN A 132 " model vdw 2.237 3.040 nonbonded pdb=" OG SER A 755 " pdb=" OG1 THR A 758 " model vdw 2.251 3.040 ... (remaining 67841 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.600 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 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 0.053 9349 Z= 0.271 Angle : 0.757 11.839 12690 Z= 0.435 Chirality : 0.056 0.548 1498 Planarity : 0.005 0.066 1615 Dihedral : 16.656 118.691 3490 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.16 % Favored : 90.30 % Rotamer: Outliers : 1.29 % Allowed : 0.50 % Favored : 98.22 % Cbeta Deviations : 0.55 % 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 (0.25), residues: 1124 helix: 1.37 (0.33), residues: 272 sheet: -0.07 (0.39), residues: 181 loop : -2.05 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 433 HIS 0.004 0.001 HIS B 951 PHE 0.037 0.001 PHE B 371 TYR 0.031 0.001 TYR B 450 ARG 0.015 0.001 ARG B1016 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.940 Fit side-chains REVERT: A 290 LEU cc_start: 0.8808 (tt) cc_final: 0.8282 (tt) REVERT: B 446 TYR cc_start: 0.6764 (OUTLIER) cc_final: 0.6471 (t80) REVERT: B 490 ARG cc_start: 0.8319 (mtt90) cc_final: 0.7178 (tpm170) REVERT: B 770 GLU cc_start: 0.6475 (tm-30) cc_final: 0.6274 (tm-30) REVERT: B 999 GLN cc_start: 0.8453 (tm-30) cc_final: 0.7871 (tm-30) outliers start: 13 outliers final: 4 residues processed: 120 average time/residue: 0.2029 time to fit residues: 34.7910 Evaluate side-chains 75 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 PRO Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 491 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN B 687 GLN B 962 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 9349 Z= 0.406 Angle : 0.774 11.451 12690 Z= 0.397 Chirality : 0.049 0.339 1498 Planarity : 0.005 0.074 1615 Dihedral : 12.876 112.316 1434 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.68 % Favored : 89.15 % Rotamer: Outliers : 1.49 % Allowed : 10.80 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.24), residues: 1124 helix: 1.20 (0.31), residues: 269 sheet: -0.30 (0.39), residues: 170 loop : -2.45 (0.21), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 630 HIS 0.008 0.001 HIS A 622 PHE 0.030 0.002 PHE B 556 TYR 0.017 0.002 TYR A 276 ARG 0.005 0.001 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: A 629 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8076 (t) REVERT: A 773 LYS cc_start: 0.9096 (tptt) cc_final: 0.8857 (tptp) REVERT: A 833 GLN cc_start: 0.8302 (tp-100) cc_final: 0.8079 (tp-100) REVERT: B 446 TYR cc_start: 0.7012 (OUTLIER) cc_final: 0.6696 (t80) REVERT: B 449 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7883 (pp) REVERT: B 490 ARG cc_start: 0.8281 (mtt90) cc_final: 0.7036 (tpm170) REVERT: B 999 GLN cc_start: 0.8558 (tm-30) cc_final: 0.7935 (tm-30) REVERT: B 1009 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8995 (mt) outliers start: 15 outliers final: 6 residues processed: 89 average time/residue: 0.2048 time to fit residues: 26.5577 Evaluate side-chains 77 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 1009 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.3980 chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 35 optimal weight: 0.0030 chunk 83 optimal weight: 0.8980 overall best weight: 1.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9349 Z= 0.201 Angle : 0.652 9.874 12690 Z= 0.328 Chirality : 0.046 0.371 1498 Planarity : 0.004 0.057 1615 Dihedral : 11.906 112.061 1428 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.34 % Favored : 90.48 % Rotamer: Outliers : 1.88 % Allowed : 14.67 % Favored : 83.45 % 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: -1.32 (0.25), residues: 1124 helix: 1.64 (0.32), residues: 263 sheet: -0.04 (0.42), residues: 160 loop : -2.25 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 630 HIS 0.003 0.001 HIS A 622 PHE 0.015 0.001 PHE B 371 TYR 0.013 0.001 TYR B 492 ARG 0.004 0.000 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.886 Fit side-chains REVERT: A 290 LEU cc_start: 0.8779 (tt) cc_final: 0.8543 (tp) REVERT: A 737 MET cc_start: 0.7546 (ttm) cc_final: 0.7157 (tpp) REVERT: A 770 GLU cc_start: 0.8579 (tt0) cc_final: 0.7881 (tt0) REVERT: A 833 GLN cc_start: 0.8250 (tp-100) cc_final: 0.7919 (tp-100) REVERT: B 446 TYR cc_start: 0.6896 (OUTLIER) cc_final: 0.6537 (t80) REVERT: B 490 ARG cc_start: 0.8056 (mtt90) cc_final: 0.6804 (tpm170) REVERT: B 737 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7952 (tpp) REVERT: B 999 GLN cc_start: 0.8489 (tm-30) cc_final: 0.7858 (tm-30) outliers start: 19 outliers final: 11 residues processed: 93 average time/residue: 0.1932 time to fit residues: 26.4434 Evaluate side-chains 80 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 737 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 111 optimal weight: 0.1980 chunk 99 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9349 Z= 0.336 Angle : 0.713 9.356 12690 Z= 0.363 Chirality : 0.047 0.325 1498 Planarity : 0.005 0.071 1615 Dihedral : 11.289 113.718 1428 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.30 % Favored : 88.52 % Rotamer: Outliers : 2.28 % Allowed : 17.24 % Favored : 80.48 % 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: -1.62 (0.24), residues: 1124 helix: 1.38 (0.32), residues: 269 sheet: -0.28 (0.40), residues: 157 loop : -2.45 (0.21), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 630 HIS 0.004 0.001 HIS A 622 PHE 0.017 0.002 PHE B 556 TYR 0.013 0.002 TYR B 348 ARG 0.004 0.001 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 1.045 Fit side-chains REVERT: A 290 LEU cc_start: 0.8745 (tt) cc_final: 0.8449 (tp) REVERT: A 773 LYS cc_start: 0.9152 (tptt) cc_final: 0.8420 (tptt) REVERT: A 833 GLN cc_start: 0.8306 (tp-100) cc_final: 0.7942 (tp-100) REVERT: B 415 ILE cc_start: 0.8374 (mp) cc_final: 0.7908 (tp) REVERT: B 446 TYR cc_start: 0.6955 (OUTLIER) cc_final: 0.6618 (t80) REVERT: B 490 ARG cc_start: 0.8152 (mtt90) cc_final: 0.7021 (tpm170) REVERT: B 770 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7846 (tt0) REVERT: B 999 GLN cc_start: 0.8529 (tm-30) cc_final: 0.7905 (tm-30) outliers start: 23 outliers final: 16 residues processed: 92 average time/residue: 0.1989 time to fit residues: 26.5319 Evaluate side-chains 83 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 737 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 94 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9349 Z= 0.203 Angle : 0.650 10.192 12690 Z= 0.328 Chirality : 0.046 0.327 1498 Planarity : 0.004 0.055 1615 Dihedral : 10.674 111.247 1428 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.43 % Favored : 90.30 % Rotamer: Outliers : 2.38 % Allowed : 18.83 % Favored : 78.79 % 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: -1.40 (0.24), residues: 1124 helix: 1.64 (0.32), residues: 263 sheet: 0.11 (0.43), residues: 141 loop : -2.32 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 630 HIS 0.002 0.001 HIS A1055 PHE 0.010 0.001 PHE B 371 TYR 0.012 0.001 TYR B 492 ARG 0.005 0.000 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 1.100 Fit side-chains REVERT: A 290 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8463 (tp) REVERT: A 300 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8368 (tt) REVERT: A 773 LYS cc_start: 0.9001 (tptt) cc_final: 0.8779 (tptt) REVERT: A 833 GLN cc_start: 0.8269 (tp-100) cc_final: 0.7859 (tp-100) REVERT: B 412 THR cc_start: 0.7772 (OUTLIER) cc_final: 0.7444 (t) REVERT: B 415 ILE cc_start: 0.8408 (mp) cc_final: 0.7916 (tp) REVERT: B 446 TYR cc_start: 0.7070 (OUTLIER) cc_final: 0.6700 (t80) REVERT: B 490 ARG cc_start: 0.8052 (mtt90) cc_final: 0.6892 (tpm170) REVERT: B 737 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7740 (tpp) REVERT: B 770 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7779 (tt0) REVERT: B 999 GLN cc_start: 0.8472 (tm-30) cc_final: 0.7800 (tm-30) REVERT: B 1009 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8979 (mp) outliers start: 24 outliers final: 12 residues processed: 95 average time/residue: 0.2052 time to fit residues: 28.3379 Evaluate side-chains 86 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 1009 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.3980 chunk 21 optimal weight: 6.9990 chunk 65 optimal weight: 0.0770 chunk 27 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN B 748 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9349 Z= 0.175 Angle : 0.628 10.016 12690 Z= 0.312 Chirality : 0.045 0.325 1498 Planarity : 0.004 0.051 1615 Dihedral : 10.035 108.566 1428 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.61 % Favored : 90.21 % Rotamer: Outliers : 2.48 % Allowed : 19.23 % Favored : 78.30 % 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: -1.26 (0.25), residues: 1124 helix: 1.92 (0.34), residues: 257 sheet: 0.19 (0.44), residues: 141 loop : -2.27 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 630 HIS 0.002 0.001 HIS A 202 PHE 0.009 0.001 PHE B 371 TYR 0.009 0.001 TYR B 348 ARG 0.007 0.000 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 290 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8474 (tp) REVERT: A 622 HIS cc_start: 0.4370 (p-80) cc_final: 0.3999 (p-80) REVERT: A 737 MET cc_start: 0.7498 (ttm) cc_final: 0.7190 (tpp) REVERT: A 773 LYS cc_start: 0.9097 (tptt) cc_final: 0.8433 (tppt) REVERT: A 833 GLN cc_start: 0.8104 (tp-100) cc_final: 0.7675 (tp-100) REVERT: B 303 PHE cc_start: 0.7222 (m-80) cc_final: 0.7011 (t80) REVERT: B 415 ILE cc_start: 0.8362 (mp) cc_final: 0.7891 (tp) REVERT: B 446 TYR cc_start: 0.7081 (OUTLIER) cc_final: 0.6772 (t80) REVERT: B 490 ARG cc_start: 0.7963 (mtt90) cc_final: 0.6933 (tpm170) REVERT: B 737 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7697 (tpp) REVERT: B 770 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7777 (tt0) REVERT: B 999 GLN cc_start: 0.8439 (tm-30) cc_final: 0.7812 (tm-30) REVERT: B 1009 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.9008 (mp) outliers start: 25 outliers final: 13 residues processed: 99 average time/residue: 0.2111 time to fit residues: 30.0358 Evaluate side-chains 87 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 1009 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 68 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 9349 Z= 0.365 Angle : 0.728 10.071 12690 Z= 0.371 Chirality : 0.048 0.317 1498 Planarity : 0.005 0.065 1615 Dihedral : 10.018 109.588 1428 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.01 % Favored : 87.81 % Rotamer: Outliers : 3.27 % Allowed : 21.01 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.24), residues: 1124 helix: 1.37 (0.32), residues: 268 sheet: -0.27 (0.41), residues: 159 loop : -2.45 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 630 HIS 0.004 0.001 HIS A 622 PHE 0.017 0.002 PHE B 540 TYR 0.013 0.002 TYR A 276 ARG 0.005 0.001 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 74 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 290 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8636 (tp) REVERT: A 300 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8415 (tt) REVERT: A 622 HIS cc_start: 0.4275 (OUTLIER) cc_final: 0.3913 (p-80) REVERT: A 833 GLN cc_start: 0.8132 (tp-100) cc_final: 0.7707 (tp-100) REVERT: B 415 ILE cc_start: 0.8378 (mp) cc_final: 0.7897 (tp) REVERT: B 490 ARG cc_start: 0.8185 (mtt90) cc_final: 0.7120 (tpm170) REVERT: B 737 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7805 (tpp) REVERT: B 767 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8324 (pp) REVERT: B 999 GLN cc_start: 0.8555 (tm-30) cc_final: 0.7927 (tm-30) REVERT: B 1009 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9034 (mp) outliers start: 33 outliers final: 20 residues processed: 100 average time/residue: 0.1966 time to fit residues: 28.5161 Evaluate side-chains 94 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 1009 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.0020 chunk 70 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 96 optimal weight: 0.1980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9349 Z= 0.182 Angle : 0.683 11.476 12690 Z= 0.341 Chirality : 0.046 0.327 1498 Planarity : 0.004 0.048 1615 Dihedral : 9.940 107.466 1426 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.96 % Favored : 89.86 % Rotamer: Outliers : 2.18 % Allowed : 21.90 % Favored : 75.92 % 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: -1.41 (0.25), residues: 1124 helix: 1.61 (0.33), residues: 262 sheet: -0.03 (0.42), residues: 152 loop : -2.31 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 630 HIS 0.004 0.001 HIS A 242 PHE 0.019 0.001 PHE A 756 TYR 0.012 0.001 TYR B 492 ARG 0.008 0.001 ARG B 980 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 290 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8526 (tp) REVERT: A 300 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8368 (tt) REVERT: A 622 HIS cc_start: 0.4338 (OUTLIER) cc_final: 0.3970 (p-80) REVERT: A 753 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.7987 (t80) REVERT: B 415 ILE cc_start: 0.8350 (mp) cc_final: 0.7858 (tp) REVERT: B 446 TYR cc_start: 0.7011 (OUTLIER) cc_final: 0.6607 (t80) REVERT: B 490 ARG cc_start: 0.8059 (mtt90) cc_final: 0.7017 (tpm170) REVERT: B 737 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7751 (tpp) REVERT: B 999 GLN cc_start: 0.8456 (tm-30) cc_final: 0.7789 (tm-30) REVERT: B 1009 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8997 (mp) outliers start: 22 outliers final: 13 residues processed: 90 average time/residue: 0.2032 time to fit residues: 26.6343 Evaluate side-chains 89 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 1009 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9349 Z= 0.242 Angle : 0.713 10.795 12690 Z= 0.360 Chirality : 0.049 0.395 1498 Planarity : 0.005 0.054 1615 Dihedral : 9.662 107.693 1425 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.85 % Favored : 88.88 % Rotamer: Outliers : 2.08 % Allowed : 22.20 % Favored : 75.72 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.49 (0.25), residues: 1124 helix: 1.53 (0.33), residues: 268 sheet: -0.13 (0.42), residues: 149 loop : -2.38 (0.21), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 630 HIS 0.002 0.001 HIS A 242 PHE 0.019 0.001 PHE A 756 TYR 0.011 0.001 TYR B 492 ARG 0.008 0.000 ARG B 980 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 300 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8442 (tt) REVERT: A 622 HIS cc_start: 0.4332 (OUTLIER) cc_final: 0.3959 (p-80) REVERT: A 753 TYR cc_start: 0.8600 (OUTLIER) cc_final: 0.8132 (t80) REVERT: B 415 ILE cc_start: 0.8380 (mp) cc_final: 0.7886 (tp) REVERT: B 446 TYR cc_start: 0.7046 (OUTLIER) cc_final: 0.6628 (t80) REVERT: B 490 ARG cc_start: 0.8107 (mtt90) cc_final: 0.7067 (tpm170) REVERT: B 737 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7794 (tpp) REVERT: B 770 GLU cc_start: 0.7740 (pt0) cc_final: 0.7485 (tt0) REVERT: B 999 GLN cc_start: 0.8476 (tm-30) cc_final: 0.7807 (tm-30) REVERT: B 1009 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.9024 (mp) outliers start: 21 outliers final: 14 residues processed: 84 average time/residue: 0.2024 time to fit residues: 24.9292 Evaluate side-chains 87 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 1009 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9349 Z= 0.194 Angle : 0.688 12.370 12690 Z= 0.346 Chirality : 0.047 0.351 1498 Planarity : 0.005 0.049 1615 Dihedral : 9.547 106.757 1425 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.05 % Favored : 89.68 % Rotamer: Outliers : 1.88 % Allowed : 22.60 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.44 (0.25), residues: 1124 helix: 1.58 (0.33), residues: 264 sheet: -0.02 (0.44), residues: 144 loop : -2.33 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 630 HIS 0.003 0.001 HIS A 242 PHE 0.015 0.001 PHE A 756 TYR 0.010 0.001 TYR A 155 ARG 0.008 0.000 ARG A 762 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8367 (tt) REVERT: A 622 HIS cc_start: 0.4313 (OUTLIER) cc_final: 0.3938 (p-80) REVERT: A 753 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.8249 (t80) REVERT: B 415 ILE cc_start: 0.8381 (mp) cc_final: 0.7851 (tp) REVERT: B 446 TYR cc_start: 0.7021 (OUTLIER) cc_final: 0.6629 (t80) REVERT: B 490 ARG cc_start: 0.8074 (mtt90) cc_final: 0.7040 (tpm170) REVERT: B 737 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7682 (tpp) REVERT: B 770 GLU cc_start: 0.7709 (pt0) cc_final: 0.7433 (tt0) REVERT: B 999 GLN cc_start: 0.8466 (tm-30) cc_final: 0.7791 (tm-30) REVERT: B 1009 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9016 (mp) outliers start: 19 outliers final: 13 residues processed: 87 average time/residue: 0.2134 time to fit residues: 27.0216 Evaluate side-chains 92 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 1009 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 0.0270 chunk 38 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 GLN B 962 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.113682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.088530 restraints weight = 28569.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.088528 restraints weight = 18395.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.089308 restraints weight = 15426.380| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9349 Z= 0.315 Angle : 0.739 10.964 12690 Z= 0.375 Chirality : 0.048 0.336 1498 Planarity : 0.005 0.057 1615 Dihedral : 9.652 108.619 1425 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.48 % Favored : 88.26 % Rotamer: Outliers : 1.98 % Allowed : 22.50 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.66 (0.24), residues: 1124 helix: 1.46 (0.33), residues: 262 sheet: -0.30 (0.41), residues: 156 loop : -2.48 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 630 HIS 0.008 0.001 HIS B 622 PHE 0.019 0.002 PHE B 540 TYR 0.012 0.002 TYR A 276 ARG 0.008 0.001 ARG A 762 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1747.78 seconds wall clock time: 33 minutes 4.25 seconds (1984.25 seconds total)