Starting phenix.real_space_refine on Fri Jul 3 01:35:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8b8q_15919/07_2026/8b8q_15919.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b8q_15919/07_2026/8b8q_15919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8b8q_15919/07_2026/8b8q_15919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b8q_15919/07_2026/8b8q_15919.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8b8q_15919/07_2026/8b8q_15919.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8b8q_15919/07_2026/8b8q_15919.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8b8q_15919/07_2026/8b8q_15919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b8q_15919/07_2026/8b8q_15919.map" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 74 5.16 5 C 7480 2.51 5 N 1834 2.21 5 O 1976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11370 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5682 Classifications: {'peptide': 691} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 31, 'TRANS': 659} Chain breaks: 8 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5682 Classifications: {'peptide': 691} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 31, 'TRANS': 659} Chain breaks: 8 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.28, per 1000 atoms: 0.20 Number of scatterers: 11370 At special positions: 0 Unit cell: (74.214, 113.274, 128.247, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 74 16.00 O 1976 8.00 N 1834 7.00 C 7480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.04 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " 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 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 455.5 milliseconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2624 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 4 sheets defined 65.4% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 90 through 109 removed outlier: 3.505A pdb=" N GLY A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 205 through 220 Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 284 through 292 removed outlier: 3.617A pdb=" N ARG A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 327 Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 362 through 375 removed outlier: 4.280A pdb=" N GLU A 366 " --> pdb=" O ASN A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 409 Processing helix chain 'A' and resid 447 through 484 removed outlier: 3.654A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 538 removed outlier: 3.799A pdb=" N THR A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE A 538 " --> pdb=" O MET A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 573 removed outlier: 3.855A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 638 Proline residue: A 628 - end of helix Processing helix chain 'A' and resid 648 through 655 Processing helix chain 'A' and resid 662 through 681 removed outlier: 3.697A pdb=" N GLU A 667 " --> pdb=" O GLY A 663 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.922A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 796 through 802 removed outlier: 4.496A pdb=" N GLY A 800 " --> pdb=" O ASN A 796 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 801 " --> pdb=" O PRO A 797 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY A 802 " --> pdb=" O TYR A 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 796 through 802' Processing helix chain 'A' and resid 825 through 857 Processing helix chain 'A' and resid 861 through 870 Processing helix chain 'B' and resid 90 through 109 removed outlier: 3.514A pdb=" N GLY B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 205 through 220 Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 284 through 292 removed outlier: 3.660A pdb=" N ARG B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 327 Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 362 through 375 removed outlier: 4.264A pdb=" N GLU B 366 " --> pdb=" O ASN B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 409 Processing helix chain 'B' and resid 447 through 484 removed outlier: 3.788A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 538 removed outlier: 3.772A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE B 538 " --> pdb=" O MET B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 3.750A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE B 570 " --> pdb=" O SER B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 638 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 648 through 655 Processing helix chain 'B' and resid 662 through 681 removed outlier: 3.785A pdb=" N TYR B 666 " --> pdb=" O LEU B 662 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 4.050A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 746 Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 797 through 802 removed outlier: 3.911A pdb=" N LEU B 801 " --> pdb=" O PRO B 797 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY B 802 " --> pdb=" O TYR B 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 797 through 802' Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 870 Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 116 removed outlier: 3.592A pdb=" N ALA A 244 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 782 through 785 Processing sheet with id=AA3, first strand: chain 'B' and resid 111 through 116 removed outlier: 3.601A pdb=" N ALA B 244 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 782 through 785 715 hydrogen bonds defined for protein. 2109 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3454 1.34 - 1.46: 2819 1.46 - 1.58: 5291 1.58 - 1.69: 0 1.69 - 1.81: 110 Bond restraints: 11674 Sorted by residual: bond pdb=" C GLU B 272 " pdb=" N TRP B 273 " ideal model delta sigma weight residual 1.332 1.312 0.021 1.40e-02 5.10e+03 2.21e+00 bond pdb=" CA PRO A 815 " pdb=" C PRO A 815 " ideal model delta sigma weight residual 1.517 1.507 0.010 6.70e-03 2.23e+04 2.18e+00 bond pdb=" C GLY B 582 " pdb=" O GLY B 582 " ideal model delta sigma weight residual 1.243 1.230 0.012 9.30e-03 1.16e+04 1.74e+00 bond pdb=" C ASN B 562 " pdb=" O ASN B 562 " ideal model delta sigma weight residual 1.235 1.251 -0.016 1.26e-02 6.30e+03 1.57e+00 bond pdb=" C ASN A 562 " pdb=" O ASN A 562 " ideal model delta sigma weight residual 1.235 1.250 -0.014 1.26e-02 6.30e+03 1.32e+00 ... (remaining 11669 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 15658 2.05 - 4.11: 154 4.11 - 6.16: 12 6.16 - 8.21: 2 8.21 - 10.26: 2 Bond angle restraints: 15828 Sorted by residual: angle pdb=" CA LEU A 662 " pdb=" CB LEU A 662 " pdb=" CG LEU A 662 " ideal model delta sigma weight residual 116.30 126.56 -10.26 3.50e+00 8.16e-02 8.60e+00 angle pdb=" N PRO A 763 " pdb=" CA PRO A 763 " pdb=" C PRO A 763 " ideal model delta sigma weight residual 110.70 114.08 -3.38 1.22e+00 6.72e-01 7.70e+00 angle pdb=" N PRO B 763 " pdb=" CA PRO B 763 " pdb=" C PRO B 763 " ideal model delta sigma weight residual 110.70 114.04 -3.34 1.22e+00 6.72e-01 7.50e+00 angle pdb=" CA LEU B 662 " pdb=" CB LEU B 662 " pdb=" CG LEU B 662 " ideal model delta sigma weight residual 116.30 125.35 -9.05 3.50e+00 8.16e-02 6.69e+00 angle pdb=" N ILE B 786 " pdb=" CA ILE B 786 " pdb=" C ILE B 786 " ideal model delta sigma weight residual 106.21 108.60 -2.39 1.07e+00 8.73e-01 4.99e+00 ... (remaining 15823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 6264 16.25 - 32.50: 445 32.50 - 48.75: 117 48.75 - 65.00: 36 65.00 - 81.25: 2 Dihedral angle restraints: 6864 sinusoidal: 2788 harmonic: 4076 Sorted by residual: dihedral pdb=" CA THR B 787 " pdb=" C THR B 787 " pdb=" N ASP B 788 " pdb=" CA ASP B 788 " ideal model delta harmonic sigma weight residual -180.00 -158.81 -21.19 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA LYS B 590 " pdb=" C LYS B 590 " pdb=" N TYR B 591 " pdb=" CA TYR B 591 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ASN B 362 " pdb=" C ASN B 362 " pdb=" N ILE B 363 " pdb=" CA ILE B 363 " ideal model delta harmonic sigma weight residual 180.00 161.21 18.79 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 6861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 935 0.025 - 0.050: 471 0.050 - 0.075: 200 0.075 - 0.101: 92 0.101 - 0.126: 36 Chirality restraints: 1734 Sorted by residual: chirality pdb=" CA ILE A 762 " pdb=" N ILE A 762 " pdb=" C ILE A 762 " pdb=" CB ILE A 762 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA ILE B 74 " pdb=" N ILE B 74 " pdb=" C ILE B 74 " pdb=" CB ILE B 74 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA ILE A 74 " pdb=" N ILE A 74 " pdb=" C ILE A 74 " pdb=" CB ILE A 74 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 1731 not shown) Planarity restraints: 1958 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 612 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.67e+00 pdb=" C ILE A 612 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE A 612 " -0.014 2.00e-02 2.50e+03 pdb=" N MET A 613 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 612 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.48e+00 pdb=" C ILE B 612 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE B 612 " -0.014 2.00e-02 2.50e+03 pdb=" N MET B 613 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 613 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C MET A 613 " -0.033 2.00e-02 2.50e+03 pdb=" O MET A 613 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY A 614 " 0.011 2.00e-02 2.50e+03 ... (remaining 1955 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 254 2.68 - 3.24: 11651 3.24 - 3.79: 18977 3.79 - 4.35: 23980 4.35 - 4.90: 40101 Nonbonded interactions: 94963 Sorted by model distance: nonbonded pdb=" OG SER B 782 " pdb=" O ASP B 811 " model vdw 2.126 3.040 nonbonded pdb=" OD2 ASP A 749 " pdb=" OH TYR A 776 " model vdw 2.152 3.040 nonbonded pdb=" OE1 GLU A 667 " pdb="CA CA A1002 " model vdw 2.189 2.510 nonbonded pdb=" OG SER A 782 " pdb=" O ASP A 811 " model vdw 2.196 3.040 nonbonded pdb=" OE2 GLU B 670 " pdb="CA CA B1001 " model vdw 2.229 2.510 ... (remaining 94958 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.360 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.160 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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 0.043 11680 Z= 0.183 Angle : 0.542 10.263 15840 Z= 0.302 Chirality : 0.039 0.126 1734 Planarity : 0.004 0.043 1958 Dihedral : 12.629 81.250 4222 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 7.93 % Allowed : 7.61 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.23), residues: 1346 helix: 1.68 (0.17), residues: 812 sheet: 1.14 (0.71), residues: 54 loop : -1.33 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 813 TYR 0.014 0.001 TYR A 580 PHE 0.014 0.001 PHE A 556 TRP 0.018 0.001 TRP A 397 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (11674) covalent geometry : angle 0.54234 / 0.30 (15828) SS BOND : bond 0.00287 / 0.14 ( 6) SS BOND : angle 0.66812 / 0.40 ( 12) hydrogen bonds : bond 0.13280 / 8.57 ( 715) hydrogen bonds : angle 5.66342 / 3.85 ( 2109) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 215 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.7988 (m-80) REVERT: A 272 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7744 (tm-30) REVERT: A 327 ASP cc_start: 0.8159 (m-30) cc_final: 0.7950 (m-30) REVERT: A 365 CYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7790 (t) REVERT: A 370 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7823 (mtmt) REVERT: A 472 ILE cc_start: 0.7612 (mt) cc_final: 0.7398 (pt) REVERT: A 530 LYS cc_start: 0.8992 (mmtm) cc_final: 0.8646 (mtmt) REVERT: A 534 MET cc_start: 0.8316 (mmt) cc_final: 0.7972 (tmm) REVERT: A 588 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6255 (pp) REVERT: A 613 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7548 (mmt) REVERT: A 772 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8331 (p) REVERT: A 785 ASN cc_start: 0.5675 (OUTLIER) cc_final: 0.5425 (p0) REVERT: A 855 TYR cc_start: 0.8258 (t80) cc_final: 0.7672 (t80) REVERT: A 862 LYS cc_start: 0.7175 (OUTLIER) cc_final: 0.6830 (pmtt) REVERT: B 93 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8355 (ptpt) REVERT: B 271 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7278 (mmm160) REVERT: B 290 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8382 (pptt) REVERT: B 295 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7716 (mtpt) REVERT: B 352 CYS cc_start: 0.7732 (t) cc_final: 0.6759 (p) REVERT: B 365 CYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6662 (t) REVERT: B 395 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8328 (mp0) REVERT: B 409 ASP cc_start: 0.8661 (m-30) cc_final: 0.7602 (t0) REVERT: B 524 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8006 (pp) REVERT: B 534 MET cc_start: 0.7440 (mmt) cc_final: 0.6687 (ttm) REVERT: B 657 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7451 (mm-40) REVERT: B 714 MET cc_start: 0.8245 (mtm) cc_final: 0.7704 (mpm) REVERT: B 750 MET cc_start: 0.8771 (ttm) cc_final: 0.8055 (tpt) REVERT: B 773 MET cc_start: 0.8830 (mmt) cc_final: 0.8464 (tpt) REVERT: B 788 ASP cc_start: 0.6648 (OUTLIER) cc_final: 0.3723 (t0) REVERT: B 843 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8661 (mt-10) outliers start: 98 outliers final: 24 residues processed: 296 average time/residue: 0.5175 time to fit residues: 165.7039 Evaluate side-chains 170 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 730 GLN Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 GLN B 108 HIS ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 GLN B 710 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.140761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.105034 restraints weight = 20879.476| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.94 r_work: 0.3291 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11680 Z= 0.240 Angle : 0.642 9.994 15840 Z= 0.346 Chirality : 0.043 0.141 1734 Planarity : 0.005 0.043 1958 Dihedral : 8.522 58.548 1607 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 7.04 % Allowed : 14.32 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.23), residues: 1346 helix: 1.50 (0.17), residues: 814 sheet: -0.04 (0.60), residues: 64 loop : -1.23 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 98 TYR 0.016 0.002 TYR A 591 PHE 0.021 0.002 PHE A 556 TRP 0.016 0.002 TRP A 397 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.24 (11674) covalent geometry : angle 0.64087 / 0.35 (15828) SS BOND : bond 0.00366 / 0.18 ( 6) SS BOND : angle 1.26670 / 0.74 ( 12) hydrogen bonds : bond 0.06488 / 4.20 ( 715) hydrogen bonds : angle 5.18771 / 3.56 ( 2109) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 142 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.7630 (m-80) REVERT: A 234 ASN cc_start: 0.9389 (t0) cc_final: 0.9187 (p0) REVERT: A 365 CYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7799 (t) REVERT: A 369 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7624 (mtmm) REVERT: A 370 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7773 (mtmt) REVERT: A 530 LYS cc_start: 0.8952 (mmtm) cc_final: 0.8670 (mttt) REVERT: A 548 GLU cc_start: 0.8172 (pt0) cc_final: 0.7899 (pt0) REVERT: A 588 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6373 (pp) REVERT: A 613 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7500 (mmt) REVERT: A 720 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8441 (pt0) REVERT: A 785 ASN cc_start: 0.5949 (OUTLIER) cc_final: 0.5742 (p0) REVERT: A 812 PHE cc_start: 0.8239 (m-80) cc_final: 0.7765 (m-80) REVERT: A 855 TYR cc_start: 0.8264 (t80) cc_final: 0.7852 (t80) REVERT: A 862 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6716 (pmtt) REVERT: B 73 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7280 (m-80) REVERT: B 93 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8264 (ptmm) REVERT: B 271 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7672 (mmm160) REVERT: B 286 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8400 (t0) REVERT: B 290 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8429 (pptt) REVERT: B 352 CYS cc_start: 0.7743 (t) cc_final: 0.7008 (p) REVERT: B 363 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7411 (mp) REVERT: B 365 CYS cc_start: 0.7262 (OUTLIER) cc_final: 0.6754 (t) REVERT: B 395 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8382 (mp0) REVERT: B 409 ASP cc_start: 0.8682 (m-30) cc_final: 0.7625 (t0) REVERT: B 524 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8066 (pp) REVERT: B 534 MET cc_start: 0.7413 (mmt) cc_final: 0.6637 (ttm) REVERT: B 750 MET cc_start: 0.8893 (ttm) cc_final: 0.8156 (tpt) REVERT: B 773 MET cc_start: 0.8760 (mmt) cc_final: 0.8356 (tpt) REVERT: B 843 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8625 (mt-10) REVERT: B 855 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.7337 (t80) outliers start: 87 outliers final: 35 residues processed: 208 average time/residue: 0.4060 time to fit residues: 93.4681 Evaluate side-chains 176 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 122 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 720 GLN Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 730 GLN Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 855 TYR Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 41 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 3 optimal weight: 0.2980 chunk 6 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 78 optimal weight: 0.0040 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 ASN A 94 GLN A 785 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.144250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.108839 restraints weight = 20918.093| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.95 r_work: 0.3348 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11680 Z= 0.143 Angle : 0.560 9.072 15840 Z= 0.302 Chirality : 0.040 0.168 1734 Planarity : 0.004 0.043 1958 Dihedral : 8.091 59.333 1598 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.99 % Allowed : 15.21 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.23), residues: 1346 helix: 1.57 (0.17), residues: 814 sheet: -0.18 (0.60), residues: 64 loop : -1.29 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 354 TYR 0.014 0.001 TYR A 586 PHE 0.017 0.001 PHE A 556 TRP 0.016 0.001 TRP B 463 HIS 0.002 0.000 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (11674) covalent geometry : angle 0.56030 / 0.30 (15828) SS BOND : bond 0.00246 / 0.12 ( 6) SS BOND : angle 0.58094 / 0.34 ( 12) hydrogen bonds : bond 0.05758 / 3.74 ( 715) hydrogen bonds : angle 4.97353 / 3.42 ( 2109) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 136 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.7330 (m-80) REVERT: A 370 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7708 (mtmt) REVERT: A 472 ILE cc_start: 0.7407 (mt) cc_final: 0.7168 (pt) REVERT: A 534 MET cc_start: 0.8326 (tmm) cc_final: 0.8074 (tmm) REVERT: A 548 GLU cc_start: 0.8239 (pt0) cc_final: 0.8033 (pt0) REVERT: A 613 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7499 (mmt) REVERT: A 812 PHE cc_start: 0.8229 (m-80) cc_final: 0.7778 (m-80) REVERT: A 852 PHE cc_start: 0.8146 (m-10) cc_final: 0.7929 (m-10) REVERT: A 855 TYR cc_start: 0.8190 (t80) cc_final: 0.7835 (t80) REVERT: B 73 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7108 (m-80) REVERT: B 93 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8311 (ptmm) REVERT: B 216 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7679 (mp) REVERT: B 286 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8096 (p0) REVERT: B 290 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8497 (pptt) REVERT: B 322 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7779 (mm) REVERT: B 329 ASP cc_start: 0.8226 (p0) cc_final: 0.7907 (p0) REVERT: B 365 CYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6565 (t) REVERT: B 395 GLU cc_start: 0.8778 (mp0) cc_final: 0.8394 (mp0) REVERT: B 409 ASP cc_start: 0.8596 (m-30) cc_final: 0.7477 (t0) REVERT: B 524 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8003 (pp) REVERT: B 534 MET cc_start: 0.7322 (mmt) cc_final: 0.6612 (ttm) REVERT: B 750 MET cc_start: 0.8865 (ttm) cc_final: 0.8125 (tpt) REVERT: B 773 MET cc_start: 0.8840 (mmt) cc_final: 0.8331 (tpt) REVERT: B 843 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8634 (mt-10) REVERT: B 855 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.7257 (t80) outliers start: 74 outliers final: 26 residues processed: 197 average time/residue: 0.3512 time to fit residues: 76.8492 Evaluate side-chains 156 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 855 TYR Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 7 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 56 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 726 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.143383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.108558 restraints weight = 21106.488| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.95 r_work: 0.3339 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11680 Z= 0.162 Angle : 0.568 9.172 15840 Z= 0.303 Chirality : 0.041 0.184 1734 Planarity : 0.004 0.041 1958 Dihedral : 6.840 55.162 1565 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 5.74 % Allowed : 15.70 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.22), residues: 1346 helix: 1.64 (0.17), residues: 802 sheet: -0.25 (0.61), residues: 64 loop : -1.30 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 354 TYR 0.014 0.001 TYR A 586 PHE 0.034 0.001 PHE A 558 TRP 0.026 0.001 TRP B 463 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (11674) covalent geometry : angle 0.56793 / 0.30 (15828) SS BOND : bond 0.00281 / 0.14 ( 6) SS BOND : angle 0.49426 / 0.29 ( 12) hydrogen bonds : bond 0.05783 / 3.75 ( 715) hydrogen bonds : angle 4.92879 / 3.40 ( 2109) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 133 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.7379 (m-80) REVERT: A 290 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8498 (tmmt) REVERT: A 365 CYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7812 (t) REVERT: A 370 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7720 (mtmt) REVERT: A 405 GLU cc_start: 0.8428 (tt0) cc_final: 0.7777 (tp30) REVERT: A 472 ILE cc_start: 0.7368 (mt) cc_final: 0.7131 (pt) REVERT: A 534 MET cc_start: 0.8399 (tmm) cc_final: 0.8035 (tmm) REVERT: A 548 GLU cc_start: 0.8256 (pt0) cc_final: 0.8041 (pt0) REVERT: A 726 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8561 (tt0) REVERT: A 788 ASP cc_start: 0.6919 (OUTLIER) cc_final: 0.6206 (t0) REVERT: A 812 PHE cc_start: 0.8250 (m-80) cc_final: 0.7974 (m-80) REVERT: A 852 PHE cc_start: 0.8150 (m-10) cc_final: 0.7926 (m-10) REVERT: B 73 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7111 (m-80) REVERT: B 93 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8325 (ptmm) REVERT: B 271 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.6781 (tpm-80) REVERT: B 286 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8083 (p0) REVERT: B 290 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8471 (pptt) REVERT: B 322 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7861 (tm) REVERT: B 329 ASP cc_start: 0.8237 (p0) cc_final: 0.7952 (p0) REVERT: B 365 CYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6665 (t) REVERT: B 395 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8420 (mp0) REVERT: B 409 ASP cc_start: 0.8586 (m-30) cc_final: 0.7413 (t0) REVERT: B 524 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8015 (pp) REVERT: B 525 ASN cc_start: 0.8597 (m-40) cc_final: 0.7788 (m110) REVERT: B 534 MET cc_start: 0.7297 (mmt) cc_final: 0.6488 (ttm) REVERT: B 750 MET cc_start: 0.8897 (ttm) cc_final: 0.8170 (tpt) REVERT: B 773 MET cc_start: 0.8782 (mmt) cc_final: 0.8294 (tpt) REVERT: B 843 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8619 (mt-10) REVERT: B 855 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.7237 (t80) outliers start: 71 outliers final: 27 residues processed: 192 average time/residue: 0.3263 time to fit residues: 69.9127 Evaluate side-chains 165 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 122 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 726 GLN Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 855 TYR Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 35 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 90 optimal weight: 0.0980 chunk 110 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.142795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.105941 restraints weight = 20819.339| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.92 r_work: 0.3323 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11680 Z= 0.176 Angle : 0.586 9.982 15840 Z= 0.311 Chirality : 0.041 0.171 1734 Planarity : 0.004 0.041 1958 Dihedral : 6.844 58.247 1562 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 5.58 % Allowed : 16.26 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.22), residues: 1346 helix: 1.62 (0.17), residues: 802 sheet: -0.34 (0.60), residues: 64 loop : -1.32 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 354 TYR 0.017 0.001 TYR A 528 PHE 0.040 0.002 PHE A 558 TRP 0.034 0.001 TRP B 463 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 (11674) covalent geometry : angle 0.58618 / 0.31 (15828) SS BOND : bond 0.00307 / 0.14 ( 6) SS BOND : angle 0.51822 / 0.30 ( 12) hydrogen bonds : bond 0.05845 / 3.79 ( 715) hydrogen bonds : angle 4.95706 / 3.43 ( 2109) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 133 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.7495 (m-80) REVERT: A 365 CYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7756 (t) REVERT: A 369 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7680 (mtmm) REVERT: A 370 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7726 (mtmt) REVERT: A 472 ILE cc_start: 0.7368 (mt) cc_final: 0.7163 (pt) REVERT: A 534 MET cc_start: 0.8390 (tmm) cc_final: 0.8009 (tmm) REVERT: A 548 GLU cc_start: 0.8223 (pt0) cc_final: 0.7992 (pt0) REVERT: A 788 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6321 (t0) REVERT: A 852 PHE cc_start: 0.8150 (m-10) cc_final: 0.7917 (m-10) REVERT: B 73 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7112 (m-80) REVERT: B 93 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8314 (ptmm) REVERT: B 216 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7673 (mp) REVERT: B 271 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.6773 (tpm-80) REVERT: B 286 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8059 (p0) REVERT: B 290 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8415 (pptt) REVERT: B 322 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7871 (tm) REVERT: B 329 ASP cc_start: 0.8247 (p0) cc_final: 0.7963 (p0) REVERT: B 365 CYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6693 (t) REVERT: B 395 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8449 (mp0) REVERT: B 409 ASP cc_start: 0.8617 (m-30) cc_final: 0.7372 (t0) REVERT: B 521 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.9014 (tt) REVERT: B 524 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8057 (pp) REVERT: B 525 ASN cc_start: 0.8408 (m-40) cc_final: 0.8111 (m110) REVERT: B 534 MET cc_start: 0.7272 (mmt) cc_final: 0.6523 (ttm) REVERT: B 542 ARG cc_start: 0.4757 (OUTLIER) cc_final: 0.3950 (ttm170) REVERT: B 750 MET cc_start: 0.8895 (ttm) cc_final: 0.8177 (tpt) REVERT: B 773 MET cc_start: 0.8722 (mmt) cc_final: 0.8211 (tpt) REVERT: B 788 ASP cc_start: 0.6036 (OUTLIER) cc_final: 0.4376 (t0) REVERT: B 843 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8642 (mt-10) REVERT: B 855 TYR cc_start: 0.8138 (OUTLIER) cc_final: 0.7255 (t80) outliers start: 69 outliers final: 33 residues processed: 191 average time/residue: 0.3845 time to fit residues: 81.4779 Evaluate side-chains 173 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 121 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 855 TYR Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 7 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 111 GLN ** 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 = 0.3962 r_free = 0.3962 target = 0.138763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.103683 restraints weight = 21127.585| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.92 r_work: 0.3260 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 11680 Z= 0.282 Angle : 0.658 9.789 15840 Z= 0.353 Chirality : 0.045 0.254 1734 Planarity : 0.005 0.043 1958 Dihedral : 6.985 56.800 1562 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 5.99 % Allowed : 16.67 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.22), residues: 1346 helix: 1.34 (0.17), residues: 814 sheet: 0.14 (0.63), residues: 44 loop : -1.58 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 813 TYR 0.020 0.002 TYR A 586 PHE 0.032 0.002 PHE A 558 TRP 0.021 0.002 TRP B 463 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.28 (11674) covalent geometry : angle 0.65777 / 0.35 (15828) SS BOND : bond 0.00468 / 0.22 ( 6) SS BOND : angle 0.70837 / 0.41 ( 12) hydrogen bonds : bond 0.06496 / 4.19 ( 715) hydrogen bonds : angle 5.16717 / 3.59 ( 2109) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 131 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.7663 (m-80) REVERT: A 365 CYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7860 (t) REVERT: A 370 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7772 (mtmt) REVERT: A 530 LYS cc_start: 0.8940 (mmtm) cc_final: 0.8642 (mtpt) REVERT: A 534 MET cc_start: 0.8459 (tmm) cc_final: 0.8124 (tmm) REVERT: A 548 GLU cc_start: 0.8313 (pt0) cc_final: 0.8107 (pt0) REVERT: A 788 ASP cc_start: 0.7232 (OUTLIER) cc_final: 0.6437 (t0) REVERT: A 852 PHE cc_start: 0.8108 (m-10) cc_final: 0.7880 (m-10) REVERT: A 855 TYR cc_start: 0.8241 (t80) cc_final: 0.7864 (t80) REVERT: B 73 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7220 (m-80) REVERT: B 93 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8333 (ptmm) REVERT: B 216 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7702 (mp) REVERT: B 271 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.6794 (tpm-80) REVERT: B 290 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8477 (pptt) REVERT: B 329 ASP cc_start: 0.8338 (p0) cc_final: 0.8039 (p0) REVERT: B 352 CYS cc_start: 0.7914 (t) cc_final: 0.7223 (p) REVERT: B 365 CYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6853 (t) REVERT: B 395 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8436 (mp0) REVERT: B 409 ASP cc_start: 0.8693 (m-30) cc_final: 0.7360 (t0) REVERT: B 524 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8151 (pp) REVERT: B 534 MET cc_start: 0.7487 (mmt) cc_final: 0.6843 (ttt) REVERT: B 542 ARG cc_start: 0.4792 (OUTLIER) cc_final: 0.4009 (ttm170) REVERT: B 750 MET cc_start: 0.8957 (ttm) cc_final: 0.8208 (tpt) REVERT: B 773 MET cc_start: 0.8532 (mmt) cc_final: 0.8195 (tpt) REVERT: B 855 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.7335 (t80) outliers start: 74 outliers final: 36 residues processed: 190 average time/residue: 0.3928 time to fit residues: 83.3059 Evaluate side-chains 172 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 122 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 855 TYR Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 46 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 120 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 136 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 518 HIS ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 559 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.142406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.106559 restraints weight = 21162.292| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.82 r_work: 0.3359 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11680 Z= 0.167 Angle : 0.596 9.847 15840 Z= 0.320 Chirality : 0.041 0.169 1734 Planarity : 0.004 0.042 1958 Dihedral : 6.852 59.708 1561 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.34 % Allowed : 17.72 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.22), residues: 1346 helix: 1.44 (0.17), residues: 816 sheet: 0.28 (0.64), residues: 44 loop : -1.47 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 810 TYR 0.031 0.001 TYR B 77 PHE 0.030 0.001 PHE A 558 TRP 0.037 0.001 TRP B 463 HIS 0.011 0.001 HIS A 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (11674) covalent geometry : angle 0.59634 / 0.32 (15828) SS BOND : bond 0.00307 / 0.14 ( 6) SS BOND : angle 0.56323 / 0.32 ( 12) hydrogen bonds : bond 0.05855 / 3.79 ( 715) hydrogen bonds : angle 5.03651 / 3.51 ( 2109) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 130 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.7598 (m-80) REVERT: A 365 CYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7862 (t) REVERT: A 370 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7874 (mtmt) REVERT: A 534 MET cc_start: 0.8426 (tmm) cc_final: 0.8075 (tmm) REVERT: A 548 GLU cc_start: 0.8309 (pt0) cc_final: 0.8084 (pt0) REVERT: A 788 ASP cc_start: 0.6732 (OUTLIER) cc_final: 0.6284 (t0) REVERT: A 852 PHE cc_start: 0.8185 (m-10) cc_final: 0.7961 (m-10) REVERT: A 855 TYR cc_start: 0.8156 (t80) cc_final: 0.7833 (t80) REVERT: B 73 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7318 (m-80) REVERT: B 93 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8329 (ptmm) REVERT: B 286 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8393 (m-30) REVERT: B 288 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.7864 (pt) REVERT: B 290 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8509 (pptt) REVERT: B 322 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8022 (tm) REVERT: B 329 ASP cc_start: 0.8203 (p0) cc_final: 0.7955 (p0) REVERT: B 363 ILE cc_start: 0.7327 (OUTLIER) cc_final: 0.6888 (pt) REVERT: B 365 CYS cc_start: 0.7053 (OUTLIER) cc_final: 0.6669 (t) REVERT: B 386 MET cc_start: 0.9191 (tpt) cc_final: 0.8747 (tpt) REVERT: B 395 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8427 (mp0) REVERT: B 409 ASP cc_start: 0.8626 (m-30) cc_final: 0.7325 (t0) REVERT: B 524 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8140 (pp) REVERT: B 534 MET cc_start: 0.7463 (mmt) cc_final: 0.6814 (ttt) REVERT: B 750 MET cc_start: 0.8911 (ttm) cc_final: 0.8295 (tpt) REVERT: B 773 MET cc_start: 0.8720 (mmt) cc_final: 0.8166 (tpt) REVERT: B 788 ASP cc_start: 0.5585 (OUTLIER) cc_final: 0.5277 (t0) REVERT: B 855 TYR cc_start: 0.8112 (OUTLIER) cc_final: 0.7210 (t80) outliers start: 66 outliers final: 26 residues processed: 184 average time/residue: 0.3563 time to fit residues: 73.5362 Evaluate side-chains 164 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 855 TYR Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 119 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 10 optimal weight: 0.0870 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN A 518 HIS ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.142590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.106890 restraints weight = 20887.490| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.81 r_work: 0.3394 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11680 Z= 0.160 Angle : 0.601 10.158 15840 Z= 0.320 Chirality : 0.042 0.159 1734 Planarity : 0.004 0.041 1958 Dihedral : 6.744 57.379 1560 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.45 % Allowed : 19.09 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.22), residues: 1346 helix: 1.45 (0.17), residues: 818 sheet: 0.33 (0.65), residues: 44 loop : -1.47 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 478 TYR 0.026 0.001 TYR B 77 PHE 0.026 0.001 PHE A 558 TRP 0.027 0.001 TRP B 463 HIS 0.018 0.001 HIS A 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (11674) covalent geometry : angle 0.60157 / 0.32 (15828) SS BOND : bond 0.00288 / 0.13 ( 6) SS BOND : angle 0.49630 / 0.28 ( 12) hydrogen bonds : bond 0.05819 / 3.77 ( 715) hydrogen bonds : angle 5.00760 / 3.49 ( 2109) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 131 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.7601 (m-80) REVERT: A 365 CYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7889 (t) REVERT: A 370 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7970 (mtmt) REVERT: A 534 MET cc_start: 0.8409 (tmm) cc_final: 0.7980 (tmm) REVERT: A 548 GLU cc_start: 0.8326 (pt0) cc_final: 0.8100 (pt0) REVERT: A 788 ASP cc_start: 0.6622 (OUTLIER) cc_final: 0.6268 (t0) REVERT: A 852 PHE cc_start: 0.8232 (m-10) cc_final: 0.8024 (m-10) REVERT: B 73 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7354 (m-80) REVERT: B 93 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8327 (ptmm) REVERT: B 286 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8372 (m-30) REVERT: B 288 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.7861 (pt) REVERT: B 290 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8519 (pptt) REVERT: B 322 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8061 (tm) REVERT: B 329 ASP cc_start: 0.8171 (p0) cc_final: 0.7959 (p0) REVERT: B 363 ILE cc_start: 0.7335 (OUTLIER) cc_final: 0.6893 (pt) REVERT: B 365 CYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6706 (t) REVERT: B 386 MET cc_start: 0.9228 (tpt) cc_final: 0.8863 (tpt) REVERT: B 395 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8391 (mp0) REVERT: B 409 ASP cc_start: 0.8566 (m-30) cc_final: 0.7350 (t0) REVERT: B 524 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8098 (pp) REVERT: B 534 MET cc_start: 0.7385 (mmt) cc_final: 0.6814 (ttt) REVERT: B 750 MET cc_start: 0.8910 (ttm) cc_final: 0.8361 (tpt) REVERT: B 760 PHE cc_start: 0.7814 (m-80) cc_final: 0.7414 (m-10) REVERT: B 773 MET cc_start: 0.8691 (mmt) cc_final: 0.8147 (tpt) REVERT: B 855 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.7147 (t80) outliers start: 55 outliers final: 23 residues processed: 172 average time/residue: 0.3445 time to fit residues: 66.4575 Evaluate side-chains 159 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 855 TYR Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 34 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 0.0470 chunk 104 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 HIS ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 674 GLN B 695 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.143124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.107561 restraints weight = 20678.554| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.81 r_work: 0.3382 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11680 Z= 0.152 Angle : 0.611 12.808 15840 Z= 0.322 Chirality : 0.042 0.171 1734 Planarity : 0.004 0.041 1958 Dihedral : 6.284 56.899 1554 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.80 % Allowed : 20.06 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.22), residues: 1346 helix: 1.51 (0.17), residues: 818 sheet: 0.39 (0.66), residues: 44 loop : -1.38 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 478 TYR 0.026 0.001 TYR B 77 PHE 0.019 0.001 PHE A 556 TRP 0.020 0.001 TRP B 463 HIS 0.020 0.001 HIS A 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (11674) covalent geometry : angle 0.61111 / 0.32 (15828) SS BOND : bond 0.00278 / 0.13 ( 6) SS BOND : angle 0.46873 / 0.27 ( 12) hydrogen bonds : bond 0.05704 / 3.69 ( 715) hydrogen bonds : angle 4.97494 / 3.47 ( 2109) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 139 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.7552 (m-80) REVERT: A 365 CYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7831 (t) REVERT: A 370 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7861 (mtmt) REVERT: A 381 ILE cc_start: 0.8963 (mt) cc_final: 0.8719 (mt) REVERT: A 529 GLU cc_start: 0.8290 (tt0) cc_final: 0.8080 (pt0) REVERT: A 534 MET cc_start: 0.8415 (tmm) cc_final: 0.7999 (tmm) REVERT: A 548 GLU cc_start: 0.8347 (pt0) cc_final: 0.8100 (pt0) REVERT: A 558 PHE cc_start: 0.7481 (m-80) cc_final: 0.7275 (t80) REVERT: A 852 PHE cc_start: 0.8236 (m-10) cc_final: 0.8029 (m-10) REVERT: B 73 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7186 (m-80) REVERT: B 93 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8325 (ptmm) REVERT: B 286 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8403 (m-30) REVERT: B 290 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8507 (pptt) REVERT: B 322 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8035 (tm) REVERT: B 329 ASP cc_start: 0.8169 (p0) cc_final: 0.7965 (p0) REVERT: B 363 ILE cc_start: 0.7259 (OUTLIER) cc_final: 0.6829 (pt) REVERT: B 365 CYS cc_start: 0.7022 (OUTLIER) cc_final: 0.6653 (t) REVERT: B 386 MET cc_start: 0.9164 (tpt) cc_final: 0.8801 (tpt) REVERT: B 395 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8443 (mp0) REVERT: B 528 TYR cc_start: 0.7693 (OUTLIER) cc_final: 0.7341 (m-80) REVERT: B 534 MET cc_start: 0.7347 (mmt) cc_final: 0.6767 (ttt) REVERT: B 542 ARG cc_start: 0.4613 (OUTLIER) cc_final: 0.4159 (ttm110) REVERT: B 750 MET cc_start: 0.8926 (ttm) cc_final: 0.8300 (tpt) REVERT: B 760 PHE cc_start: 0.7796 (m-80) cc_final: 0.7324 (m-10) REVERT: B 855 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.7114 (t80) REVERT: B 867 LYS cc_start: 0.9096 (mtpt) cc_final: 0.8641 (mmtt) outliers start: 47 outliers final: 20 residues processed: 174 average time/residue: 0.3795 time to fit residues: 74.0564 Evaluate side-chains 163 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 855 TYR Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 HIS B 68 GLN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN B 674 GLN B 695 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.141675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.105808 restraints weight = 20911.784| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.78 r_work: 0.3350 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11680 Z= 0.201 Angle : 0.656 11.805 15840 Z= 0.347 Chirality : 0.043 0.248 1734 Planarity : 0.005 0.042 1958 Dihedral : 6.241 56.142 1552 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.16 % Allowed : 21.20 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.22), residues: 1346 helix: 1.43 (0.17), residues: 818 sheet: 0.09 (0.64), residues: 44 loop : -1.41 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 478 TYR 0.017 0.001 TYR B 654 PHE 0.033 0.002 PHE A 556 TRP 0.019 0.001 TRP B 463 HIS 0.029 0.002 HIS A 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (11674) covalent geometry : angle 0.65578 / 0.35 (15828) SS BOND : bond 0.00344 / 0.16 ( 6) SS BOND : angle 0.51672 / 0.30 ( 12) hydrogen bonds : bond 0.06037 / 3.90 ( 715) hydrogen bonds : angle 5.06365 / 3.53 ( 2109) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.7658 (m-80) REVERT: A 365 CYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7880 (t) REVERT: A 370 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7854 (mtmt) REVERT: A 529 GLU cc_start: 0.8339 (tt0) cc_final: 0.8117 (pt0) REVERT: A 534 MET cc_start: 0.8391 (tmm) cc_final: 0.7976 (tmm) REVERT: A 548 GLU cc_start: 0.8352 (pt0) cc_final: 0.8105 (pt0) REVERT: A 827 TYR cc_start: 0.7423 (t80) cc_final: 0.7048 (t80) REVERT: A 852 PHE cc_start: 0.8217 (m-10) cc_final: 0.7999 (m-10) REVERT: B 73 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7282 (m-80) REVERT: B 93 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8335 (ptmm) REVERT: B 286 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8395 (m-30) REVERT: B 288 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.7868 (pt) REVERT: B 290 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8499 (pptt) REVERT: B 322 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8056 (tm) REVERT: B 329 ASP cc_start: 0.8207 (p0) cc_final: 0.8004 (p0) REVERT: B 365 CYS cc_start: 0.7081 (OUTLIER) cc_final: 0.6751 (t) REVERT: B 386 MET cc_start: 0.9166 (tpt) cc_final: 0.8916 (tpt) REVERT: B 395 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8438 (mp0) REVERT: B 409 ASP cc_start: 0.8653 (m-30) cc_final: 0.7304 (t0) REVERT: B 524 LEU cc_start: 0.8927 (pp) cc_final: 0.8682 (pt) REVERT: B 534 MET cc_start: 0.7382 (mmt) cc_final: 0.6806 (ttt) REVERT: B 542 ARG cc_start: 0.4707 (OUTLIER) cc_final: 0.4205 (ttm170) REVERT: B 750 MET cc_start: 0.8977 (ttm) cc_final: 0.8398 (tpt) REVERT: B 760 PHE cc_start: 0.7871 (m-80) cc_final: 0.7421 (m-10) REVERT: B 855 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.7170 (t80) REVERT: B 867 LYS cc_start: 0.9097 (mtpt) cc_final: 0.8656 (mmtt) outliers start: 39 outliers final: 19 residues processed: 159 average time/residue: 0.3915 time to fit residues: 69.6658 Evaluate side-chains 151 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 855 TYR Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 22 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 HIS B 68 GLN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.141586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.105399 restraints weight = 20955.621| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.83 r_work: 0.3348 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11680 Z= 0.187 Angle : 0.660 12.010 15840 Z= 0.350 Chirality : 0.043 0.175 1734 Planarity : 0.005 0.075 1958 Dihedral : 6.098 56.297 1550 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.67 % Allowed : 21.68 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.22), residues: 1346 helix: 1.37 (0.17), residues: 822 sheet: 0.02 (0.66), residues: 44 loop : -1.39 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.032 0.001 TYR B 77 PHE 0.035 0.002 PHE A 556 TRP 0.051 0.001 TRP B 463 HIS 0.028 0.002 HIS A 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (11674) covalent geometry : angle 0.65964 / 0.35 (15828) SS BOND : bond 0.00324 / 0.15 ( 6) SS BOND : angle 0.51949 / 0.30 ( 12) hydrogen bonds : bond 0.06001 / 3.90 ( 715) hydrogen bonds : angle 5.09893 / 3.56 ( 2109) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3343.65 seconds wall clock time: 58 minutes 3.28 seconds (3483.28 seconds total)