Starting phenix.real_space_refine on Sun Jun 8 08:01:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qo9_14087/06_2025/7qo9_14087.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qo9_14087/06_2025/7qo9_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_14087/06_2025/7qo9_14087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qo9_14087/06_2025/7qo9_14087.map" model { file = "/net/cci-nas-00/data/ceres_data/7qo9_14087/06_2025/7qo9_14087.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qo9_14087/06_2025/7qo9_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-5710/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: 6.10, per 1000 atoms: 0.66 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: 2.45 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: 1.06 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: 2.54 Time building geometry restraints manager: 2.88 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: 2.760 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.860 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.000 ------------------------------------------------------------------------------- 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 9375 Z= 0.228 Angle : 0.777 11.839 12751 Z= 0.439 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00720 ( 5) link_NAG-ASN : angle 2.69980 ( 15) link_BETA1-4 : bond 0.00785 ( 4) link_BETA1-4 : angle 3.93467 ( 12) hydrogen bonds : bond 0.14730 ( 300) hydrogen bonds : angle 6.02204 ( 819) SS BOND : bond 0.00372 ( 17) SS BOND : angle 1.90374 ( 34) covalent geometry : bond 0.00410 ( 9349) covalent geometry : angle 0.75746 (12690) *********************** 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 : 0.905 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: 0.2068 time to fit residues: 35.6556 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 : 1.087 ------------------------------------------------------------------------------- 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: 10.0000 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.113845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.088519 restraints weight = 28483.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.087876 restraints weight = 20001.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.088756 restraints weight = 16222.734| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 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 9375 Z= 0.276 Angle : 0.790 11.451 12751 Z= 0.401 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 5) link_NAG-ASN : angle 2.58802 ( 15) link_BETA1-4 : bond 0.00846 ( 4) link_BETA1-4 : angle 3.27685 ( 12) hydrogen bonds : bond 0.05050 ( 300) hydrogen bonds : angle 5.71518 ( 819) SS BOND : bond 0.00501 ( 17) SS BOND : angle 1.95724 ( 34) covalent geometry : bond 0.00621 ( 9349) covalent geometry : angle 0.77412 (12690) *********************** 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 : 0.947 Fit side-chains revert: symmetry clash REVERT: A 629 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8090 (t) REVERT: A 773 LYS cc_start: 0.9138 (tptt) cc_final: 0.8890 (tptp) REVERT: A 833 GLN cc_start: 0.8283 (tp-100) cc_final: 0.8059 (tp-100) REVERT: B 446 TYR cc_start: 0.7019 (OUTLIER) cc_final: 0.6692 (t80) REVERT: B 449 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7859 (pp) REVERT: B 490 ARG cc_start: 0.8285 (mtt90) cc_final: 0.7037 (tpm170) REVERT: B 999 GLN cc_start: 0.8607 (tm-30) cc_final: 0.7989 (tm-30) REVERT: B 1009 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8992 (mt) outliers start: 15 outliers final: 6 residues processed: 89 average time/residue: 0.2026 time to fit residues: 26.1177 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 : 1.070 ------------------------------------------------------------------------------- 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 21 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 61 optimal weight: 0.0370 chunk 49 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.115811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.090655 restraints weight = 28793.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.090645 restraints weight = 18764.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.091168 restraints weight = 15327.226| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9375 Z= 0.143 Angle : 0.671 9.738 12751 Z= 0.334 Chirality : 0.046 0.367 1498 Planarity : 0.004 0.059 1615 Dihedral : 11.915 112.373 1428 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.25 % Favored : 90.57 % Rotamer: Outliers : 1.88 % Allowed : 14.97 % Favored : 83.15 % 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: -1.35 (0.25), residues: 1124 helix: 1.62 (0.32), residues: 263 sheet: -0.08 (0.41), residues: 160 loop : -2.27 (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 0.014 0.001 PHE B 371 TYR 0.015 0.001 TYR B 492 ARG 0.005 0.000 ARG A 762 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 5) link_NAG-ASN : angle 2.27927 ( 15) link_BETA1-4 : bond 0.00850 ( 4) link_BETA1-4 : angle 3.47042 ( 12) hydrogen bonds : bond 0.04456 ( 300) hydrogen bonds : angle 5.17674 ( 819) SS BOND : bond 0.00317 ( 17) SS BOND : angle 1.46012 ( 34) covalent geometry : bond 0.00321 ( 9349) covalent geometry : angle 0.65537 (12690) *********************** 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 96 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 737 MET cc_start: 0.7709 (ttm) cc_final: 0.7230 (tpp) REVERT: A 770 GLU cc_start: 0.8634 (tt0) cc_final: 0.7860 (tt0) REVERT: A 833 GLN cc_start: 0.8221 (tp-100) cc_final: 0.7890 (tp-100) REVERT: B 446 TYR cc_start: 0.6902 (OUTLIER) cc_final: 0.6532 (t80) REVERT: B 490 ARG cc_start: 0.8037 (mtt90) cc_final: 0.6765 (tpm170) REVERT: B 737 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.7914 (tpp) REVERT: B 999 GLN cc_start: 0.8551 (tm-30) cc_final: 0.7926 (tm-30) outliers start: 19 outliers final: 11 residues processed: 92 average time/residue: 0.1815 time to fit residues: 24.6936 Evaluate side-chains 78 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 101 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.114713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.089229 restraints weight = 28600.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.089522 restraints weight = 18521.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.089927 restraints weight = 15909.363| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9375 Z= 0.179 Angle : 0.684 9.467 12751 Z= 0.342 Chirality : 0.046 0.328 1498 Planarity : 0.005 0.069 1615 Dihedral : 11.164 113.271 1428 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.94 % Favored : 88.88 % Rotamer: Outliers : 2.08 % Allowed : 17.54 % Favored : 80.38 % 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: -1.42 (0.24), residues: 1124 helix: 1.60 (0.32), residues: 263 sheet: 0.10 (0.41), residues: 152 loop : -2.36 (0.21), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 630 HIS 0.004 0.001 HIS A 622 PHE 0.016 0.001 PHE B 556 TYR 0.013 0.001 TYR B 348 ARG 0.004 0.000 ARG A 762 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 5) link_NAG-ASN : angle 2.36492 ( 15) link_BETA1-4 : bond 0.00724 ( 4) link_BETA1-4 : angle 3.49589 ( 12) hydrogen bonds : bond 0.04448 ( 300) hydrogen bonds : angle 5.15835 ( 819) SS BOND : bond 0.00374 ( 17) SS BOND : angle 1.47133 ( 34) covalent geometry : bond 0.00403 ( 9349) covalent geometry : angle 0.66794 (12690) *********************** 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 100 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 1.087 Fit side-chains REVERT: A 773 LYS cc_start: 0.9178 (tptt) cc_final: 0.8434 (tptt) REVERT: A 833 GLN cc_start: 0.8244 (tp-100) cc_final: 0.7864 (tp-100) REVERT: A 987 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8844 (tm-30) REVERT: B 415 ILE cc_start: 0.8348 (mp) cc_final: 0.7880 (tp) REVERT: B 446 TYR cc_start: 0.7032 (OUTLIER) cc_final: 0.6694 (t80) REVERT: B 490 ARG cc_start: 0.8084 (mtt90) cc_final: 0.6940 (tpm170) REVERT: B 737 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7880 (tpp) REVERT: B 770 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7758 (tt0) REVERT: B 999 GLN cc_start: 0.8568 (tm-30) cc_final: 0.7921 (tm-30) outliers start: 21 outliers final: 14 residues processed: 95 average time/residue: 0.2060 time to fit residues: 28.4603 Evaluate side-chains 85 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 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 3 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 48 optimal weight: 0.0040 chunk 42 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 37 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.117024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.091575 restraints weight = 28535.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.091705 restraints weight = 18707.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.092397 restraints weight = 15976.130| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9375 Z= 0.115 Angle : 0.641 9.978 12751 Z= 0.317 Chirality : 0.045 0.327 1498 Planarity : 0.004 0.053 1615 Dihedral : 10.478 110.390 1428 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.99 % Favored : 90.75 % Rotamer: Outliers : 1.98 % Allowed : 19.33 % Favored : 78.69 % 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: -1.24 (0.25), residues: 1124 helix: 1.83 (0.33), residues: 257 sheet: 0.31 (0.44), residues: 141 loop : -2.24 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 630 HIS 0.003 0.001 HIS B 502 PHE 0.010 0.001 PHE B 371 TYR 0.009 0.001 TYR B 348 ARG 0.004 0.000 ARG A 762 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 5) link_NAG-ASN : angle 2.29409 ( 15) link_BETA1-4 : bond 0.00950 ( 4) link_BETA1-4 : angle 3.71620 ( 12) hydrogen bonds : bond 0.03927 ( 300) hydrogen bonds : angle 4.79839 ( 819) SS BOND : bond 0.00231 ( 17) SS BOND : angle 1.21521 ( 34) covalent geometry : bond 0.00254 ( 9349) covalent geometry : angle 0.62442 (12690) *********************** 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 103 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: A 622 HIS cc_start: 0.4333 (p-80) cc_final: 0.3974 (p-80) REVERT: A 833 GLN cc_start: 0.8040 (tp-100) cc_final: 0.7605 (tp-100) REVERT: A 987 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8852 (tm-30) REVERT: B 412 THR cc_start: 0.7774 (OUTLIER) cc_final: 0.7448 (t) REVERT: B 415 ILE cc_start: 0.8375 (mp) cc_final: 0.7885 (tp) REVERT: B 446 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.6678 (t80) REVERT: B 490 ARG cc_start: 0.8022 (mtt90) cc_final: 0.6919 (tpm170) REVERT: B 737 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7806 (tpp) REVERT: B 770 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7790 (tt0) REVERT: B 999 GLN cc_start: 0.8535 (tm-30) cc_final: 0.7849 (tm-30) REVERT: B 1009 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8979 (mp) outliers start: 20 outliers final: 10 residues processed: 97 average time/residue: 0.2045 time to fit residues: 28.4996 Evaluate side-chains 82 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 288 CYS 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 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 733 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 41 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 106 optimal weight: 0.2980 chunk 79 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 0.0270 chunk 98 optimal weight: 6.9990 overall best weight: 1.0440 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.115723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.089447 restraints weight = 27932.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.090381 restraints weight = 17285.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.090704 restraints weight = 13966.016| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9375 Z= 0.131 Angle : 0.645 10.323 12751 Z= 0.317 Chirality : 0.045 0.322 1498 Planarity : 0.004 0.060 1615 Dihedral : 10.094 108.563 1428 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.52 % Favored : 90.30 % Rotamer: Outliers : 2.48 % Allowed : 20.12 % Favored : 77.40 % 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: -1.27 (0.25), residues: 1124 helix: 1.86 (0.34), residues: 257 sheet: 0.22 (0.44), residues: 141 loop : -2.26 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 630 HIS 0.002 0.001 HIS B 502 PHE 0.009 0.001 PHE A 131 TYR 0.010 0.001 TYR B 348 ARG 0.006 0.000 ARG A 762 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 5) link_NAG-ASN : angle 2.23680 ( 15) link_BETA1-4 : bond 0.00885 ( 4) link_BETA1-4 : angle 3.71351 ( 12) hydrogen bonds : bond 0.03937 ( 300) hydrogen bonds : angle 4.79598 ( 819) SS BOND : bond 0.00349 ( 17) SS BOND : angle 1.43553 ( 34) covalent geometry : bond 0.00298 ( 9349) covalent geometry : angle 0.62784 (12690) *********************** 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 100 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 622 HIS cc_start: 0.4337 (p-80) cc_final: 0.3971 (p-80) REVERT: A 833 GLN cc_start: 0.8092 (tp-100) cc_final: 0.7633 (tp-100) REVERT: A 987 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8882 (tm-30) REVERT: B 415 ILE cc_start: 0.8349 (mp) cc_final: 0.7869 (tp) REVERT: B 446 TYR cc_start: 0.7156 (OUTLIER) cc_final: 0.6857 (t80) REVERT: B 490 ARG cc_start: 0.8018 (mtt90) cc_final: 0.6985 (tpm170) REVERT: B 737 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7778 (tpp) REVERT: B 770 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7841 (tt0) REVERT: B 999 GLN cc_start: 0.8558 (tm-30) cc_final: 0.7935 (tm-30) REVERT: B 1009 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.9006 (mp) outliers start: 25 outliers final: 15 residues processed: 94 average time/residue: 0.1889 time to fit residues: 26.2677 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 : 0.968 ------------------------------------------------------------------------------- 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 288 CYS 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 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 728 MET 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 7 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.116610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.089676 restraints weight = 28553.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.091107 restraints weight = 17246.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.091859 restraints weight = 12947.380| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9375 Z= 0.126 Angle : 0.647 10.501 12751 Z= 0.318 Chirality : 0.045 0.324 1498 Planarity : 0.004 0.052 1615 Dihedral : 9.722 107.713 1428 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.52 % Favored : 90.30 % Rotamer: Outliers : 2.68 % Allowed : 20.71 % Favored : 76.61 % 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: -1.31 (0.25), residues: 1124 helix: 1.73 (0.34), residues: 263 sheet: 0.19 (0.44), residues: 141 loop : -2.28 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 630 HIS 0.002 0.001 HIS A1055 PHE 0.011 0.001 PHE B 389 TYR 0.017 0.001 TYR B 492 ARG 0.006 0.000 ARG A 762 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 5) link_NAG-ASN : angle 2.22303 ( 15) link_BETA1-4 : bond 0.00754 ( 4) link_BETA1-4 : angle 3.74880 ( 12) hydrogen bonds : bond 0.03856 ( 300) hydrogen bonds : angle 4.74498 ( 819) SS BOND : bond 0.00340 ( 17) SS BOND : angle 1.45616 ( 34) covalent geometry : bond 0.00285 ( 9349) covalent geometry : angle 0.62940 (12690) *********************** 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 104 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8350 (tt) REVERT: A 622 HIS cc_start: 0.4330 (OUTLIER) cc_final: 0.3960 (p-80) REVERT: A 987 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8812 (tm-30) REVERT: B 446 TYR cc_start: 0.7010 (OUTLIER) cc_final: 0.6617 (t80) REVERT: B 490 ARG cc_start: 0.8045 (mtt90) cc_final: 0.7016 (tpm170) REVERT: B 737 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7805 (tpp) REVERT: B 999 GLN cc_start: 0.8598 (tm-30) cc_final: 0.7979 (tm-30) REVERT: B 1009 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.9023 (mp) outliers start: 27 outliers final: 15 residues processed: 98 average time/residue: 0.1869 time to fit residues: 27.0664 Evaluate side-chains 91 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 93 ILE 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 629 THR Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain B residue 390 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 64 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 80 optimal weight: 0.0470 chunk 100 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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** A 946 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.117197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.091762 restraints weight = 29087.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.092108 restraints weight = 18905.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.092548 restraints weight = 15385.782| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9375 Z= 0.117 Angle : 0.651 11.717 12751 Z= 0.318 Chirality : 0.045 0.322 1498 Planarity : 0.004 0.051 1615 Dihedral : 9.421 107.028 1428 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.07 % Favored : 90.75 % Rotamer: Outliers : 2.58 % Allowed : 21.31 % Favored : 76.11 % 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: -1.25 (0.25), residues: 1124 helix: 1.85 (0.34), residues: 257 sheet: 0.25 (0.45), residues: 136 loop : -2.23 (0.21), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 630 HIS 0.002 0.001 HIS A 202 PHE 0.011 0.001 PHE A 756 TYR 0.013 0.001 TYR B 492 ARG 0.007 0.000 ARG A 762 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 5) link_NAG-ASN : angle 2.16313 ( 15) link_BETA1-4 : bond 0.00738 ( 4) link_BETA1-4 : angle 3.76954 ( 12) hydrogen bonds : bond 0.03742 ( 300) hydrogen bonds : angle 4.67523 ( 819) SS BOND : bond 0.00332 ( 17) SS BOND : angle 1.45783 ( 34) covalent geometry : bond 0.00265 ( 9349) covalent geometry : angle 0.63347 (12690) *********************** 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 108 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7731 (tpt) cc_final: 0.7351 (tpp) REVERT: A 300 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8372 (tt) REVERT: A 622 HIS cc_start: 0.4411 (OUTLIER) cc_final: 0.4040 (p-80) REVERT: A 770 GLU cc_start: 0.8479 (tt0) cc_final: 0.8269 (tt0) REVERT: A 987 GLU cc_start: 0.9154 (tm-30) cc_final: 0.8865 (tm-30) REVERT: B 415 ILE cc_start: 0.8319 (mp) cc_final: 0.7890 (tp) REVERT: B 446 TYR cc_start: 0.7023 (OUTLIER) cc_final: 0.6628 (t80) REVERT: B 490 ARG cc_start: 0.8015 (mtt90) cc_final: 0.7021 (tpm170) REVERT: B 737 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7799 (tpp) REVERT: B 999 GLN cc_start: 0.8545 (tm-30) cc_final: 0.7855 (tm-30) REVERT: B 1009 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.9017 (mp) outliers start: 26 outliers final: 17 residues processed: 102 average time/residue: 0.2006 time to fit residues: 29.8646 Evaluate side-chains 98 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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 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 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 587 CYS Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 661 ILE 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 84 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 106 optimal weight: 0.0870 chunk 10 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.117418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.090468 restraints weight = 28430.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.092088 restraints weight = 17393.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.094293 restraints weight = 12641.476| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9375 Z= 0.119 Angle : 0.663 12.576 12751 Z= 0.325 Chirality : 0.045 0.352 1498 Planarity : 0.004 0.046 1615 Dihedral : 9.214 106.429 1427 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.52 % Favored : 90.30 % Rotamer: Outliers : 2.48 % Allowed : 21.51 % Favored : 76.02 % 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: 1.73 (0.34), residues: 263 sheet: 0.29 (0.45), residues: 136 loop : -2.23 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 630 HIS 0.002 0.001 HIS A 202 PHE 0.017 0.001 PHE A 272 TYR 0.011 0.001 TYR B 492 ARG 0.008 0.000 ARG A 762 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 5) link_NAG-ASN : angle 2.14431 ( 15) link_BETA1-4 : bond 0.00670 ( 4) link_BETA1-4 : angle 3.74154 ( 12) hydrogen bonds : bond 0.03669 ( 300) hydrogen bonds : angle 4.62426 ( 819) SS BOND : bond 0.00314 ( 17) SS BOND : angle 1.53467 ( 34) covalent geometry : bond 0.00271 ( 9349) covalent geometry : angle 0.64501 (12690) *********************** 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 106 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7622 (tpt) cc_final: 0.7254 (tpp) REVERT: A 300 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8368 (tt) REVERT: A 622 HIS cc_start: 0.4288 (OUTLIER) cc_final: 0.3937 (p-80) REVERT: A 753 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.8189 (t80) REVERT: A 773 LYS cc_start: 0.8971 (tptp) cc_final: 0.8710 (tptt) REVERT: A 987 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8682 (tm-30) REVERT: B 490 ARG cc_start: 0.8005 (mtt90) cc_final: 0.7003 (tpm170) REVERT: B 737 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7720 (tpp) REVERT: B 999 GLN cc_start: 0.8615 (tm-30) cc_final: 0.7922 (tm-30) REVERT: B 1009 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9039 (mp) outliers start: 25 outliers final: 18 residues processed: 99 average time/residue: 0.2089 time to fit residues: 29.6376 Evaluate side-chains 99 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 93 ILE Chi-restraints excluded: chain A residue 191 ASN 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 965 SER Chi-restraints excluded: chain A residue 993 LEU 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 694 MET 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 77 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 23 optimal weight: 0.0870 chunk 91 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- 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** B 406 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.117172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.088781 restraints weight = 28655.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.091038 restraints weight = 17958.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.092525 restraints weight = 13310.338| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9375 Z= 0.124 Angle : 0.669 11.972 12751 Z= 0.331 Chirality : 0.045 0.359 1498 Planarity : 0.004 0.056 1615 Dihedral : 9.067 105.866 1425 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.52 % Favored : 90.30 % Rotamer: Outliers : 2.18 % Allowed : 21.80 % Favored : 76.02 % 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: -1.25 (0.25), residues: 1124 helix: 1.86 (0.34), residues: 253 sheet: 0.36 (0.45), residues: 136 loop : -2.24 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 255 HIS 0.003 0.001 HIS B 622 PHE 0.015 0.001 PHE A 196 TYR 0.011 0.001 TYR B 492 ARG 0.008 0.000 ARG A 762 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 5) link_NAG-ASN : angle 2.08956 ( 15) link_BETA1-4 : bond 0.00603 ( 4) link_BETA1-4 : angle 3.70958 ( 12) hydrogen bonds : bond 0.03708 ( 300) hydrogen bonds : angle 4.58917 ( 819) SS BOND : bond 0.00329 ( 17) SS BOND : angle 1.54462 ( 34) covalent geometry : bond 0.00286 ( 9349) covalent geometry : angle 0.65177 (12690) ********************** 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 100 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7606 (tpt) cc_final: 0.7241 (tpp) REVERT: A 300 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8375 (tt) REVERT: A 622 HIS cc_start: 0.4225 (OUTLIER) cc_final: 0.3898 (p-80) REVERT: A 770 GLU cc_start: 0.8586 (tt0) cc_final: 0.8361 (tt0) REVERT: A 773 LYS cc_start: 0.9014 (tptp) cc_final: 0.8751 (tptt) REVERT: A 987 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8733 (tm-30) REVERT: B 490 ARG cc_start: 0.8061 (mtt90) cc_final: 0.7073 (tpm170) REVERT: B 737 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7695 (tpp) REVERT: B 999 GLN cc_start: 0.8600 (tm-30) cc_final: 0.7908 (tm-30) REVERT: B 1009 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9035 (mp) outliers start: 22 outliers final: 17 residues processed: 93 average time/residue: 0.1970 time to fit residues: 27.1343 Evaluate side-chains 98 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 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 965 SER Chi-restraints excluded: chain A residue 993 LEU 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 694 MET 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 44 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 chunk 70 optimal weight: 0.2980 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** B 962 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.116639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.091035 restraints weight = 28973.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.091709 restraints weight = 18859.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.092093 restraints weight = 14743.651| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9375 Z= 0.134 Angle : 0.670 11.640 12751 Z= 0.333 Chirality : 0.045 0.347 1498 Planarity : 0.004 0.051 1615 Dihedral : 9.003 106.642 1425 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.88 % Favored : 89.95 % Rotamer: Outliers : 2.48 % Allowed : 22.00 % Favored : 75.52 % 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: -1.34 (0.25), residues: 1124 helix: 1.74 (0.33), residues: 259 sheet: 0.26 (0.45), residues: 136 loop : -2.29 (0.21), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 630 HIS 0.003 0.001 HIS B 622 PHE 0.012 0.001 PHE A 55 TYR 0.009 0.001 TYR B 492 ARG 0.009 0.001 ARG A1016 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 5) link_NAG-ASN : angle 2.05302 ( 15) link_BETA1-4 : bond 0.00580 ( 4) link_BETA1-4 : angle 3.55521 ( 12) hydrogen bonds : bond 0.03773 ( 300) hydrogen bonds : angle 4.63350 ( 819) SS BOND : bond 0.00353 ( 17) SS BOND : angle 1.52576 ( 34) covalent geometry : bond 0.00309 ( 9349) covalent geometry : angle 0.65388 (12690) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2847.24 seconds wall clock time: 50 minutes 33.45 seconds (3033.45 seconds total)