Starting phenix.real_space_refine on Sat Aug 23 10:18:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b8q_15919/08_2025/8b8q_15919.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b8q_15919/08_2025/8b8q_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8b8q_15919/08_2025/8b8q_15919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b8q_15919/08_2025/8b8q_15919.map" model { file = "/net/cci-nas-00/data/ceres_data/8b8q_15919/08_2025/8b8q_15919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b8q_15919/08_2025/8b8q_15919.cif" } 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-2.0-5787/lib/python3.9/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: 3.46, per 1000 atoms: 0.30 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: 1.02 Conformation dependent library (CDL) restraints added in 588.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.36 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: 2.11 Time building geometry restraints manager: 1.35 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: 12.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.100 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 aren 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 covalent geometry : bond 0.00384 (11674) covalent geometry : angle 0.54234 (15828) SS BOND : bond 0.00287 ( 6) SS BOND : angle 0.66812 ( 12) hydrogen bonds : bond 0.13280 ( 715) hydrogen bonds : angle 5.66342 ( 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 : 0.487 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: 0.7705 (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: 0.5924 time to fit residues: 189.4225 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 : 0.452 ------------------------------------------------------------------------------- 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: 2.9990 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: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.139344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.103522 restraints weight = 20931.865| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.96 r_work: 0.3266 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 11680 Z= 0.292 Angle : 0.672 9.973 15840 Z= 0.363 Chirality : 0.045 0.147 1734 Planarity : 0.005 0.045 1958 Dihedral : 8.624 58.819 1607 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 7.52 % Allowed : 13.83 % 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 aren not related in a simple way. whole: 0.61 (0.22), residues: 1346 helix: 1.40 (0.17), residues: 814 sheet: 1.04 (0.66), residues: 44 loop : -1.40 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 810 TYR 0.017 0.002 TYR B 757 PHE 0.021 0.002 PHE A 556 TRP 0.017 0.002 TRP A 397 HIS 0.005 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00659 (11674) covalent geometry : angle 0.67132 (15828) SS BOND : bond 0.01025 ( 6) SS BOND : angle 1.25192 ( 12) hydrogen bonds : bond 0.06781 ( 715) hydrogen bonds : angle 5.25370 ( 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 230 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 137 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.7710 (m-80) REVERT: A 365 CYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7887 (t) REVERT: A 370 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7787 (mtmt) REVERT: A 405 GLU cc_start: 0.8512 (tt0) cc_final: 0.7808 (tp30) REVERT: A 530 LYS cc_start: 0.8951 (mmtm) cc_final: 0.8682 (mtmt) REVERT: A 548 GLU cc_start: 0.8207 (pt0) cc_final: 0.7947 (pt0) REVERT: A 588 LEU cc_start: 0.6590 (OUTLIER) cc_final: 0.6353 (pp) REVERT: A 613 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7541 (mmt) REVERT: A 720 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8233 (pt0) REVERT: A 785 ASN cc_start: 0.5992 (OUTLIER) cc_final: 0.5679 (p0) REVERT: A 812 PHE cc_start: 0.8321 (m-80) cc_final: 0.7960 (m-80) REVERT: A 855 TYR cc_start: 0.8286 (t80) cc_final: 0.7853 (t80) REVERT: A 862 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6701 (pmtt) REVERT: B 73 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7286 (m-80) REVERT: B 93 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8273 (ptmm) REVERT: B 271 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7668 (mmm160) REVERT: B 286 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8394 (t0) REVERT: B 290 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8405 (pptt) REVERT: B 352 CYS cc_start: 0.7762 (t) cc_final: 0.7053 (p) REVERT: B 365 CYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6814 (t) REVERT: B 395 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8393 (mp0) REVERT: B 409 ASP cc_start: 0.8725 (m-30) cc_final: 0.7642 (t0) REVERT: B 524 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8083 (pp) REVERT: B 530 LYS cc_start: 0.8353 (mmtm) cc_final: 0.7495 (tmtt) REVERT: B 534 MET cc_start: 0.7481 (mmt) cc_final: 0.6719 (ttm) REVERT: B 654 TYR cc_start: 0.7241 (t80) cc_final: 0.7006 (t80) REVERT: B 750 MET cc_start: 0.8933 (ttm) cc_final: 0.8204 (tpt) REVERT: B 773 MET cc_start: 0.8742 (mmt) cc_final: 0.8374 (tpt) REVERT: B 843 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8665 (mt-10) REVERT: B 855 TYR cc_start: 0.8171 (OUTLIER) cc_final: 0.7360 (t80) outliers start: 93 outliers final: 35 residues processed: 211 average time/residue: 0.4362 time to fit residues: 101.3231 Evaluate side-chains 174 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 122 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 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 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 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 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 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: 0.4980 chunk 10 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 94 GLN A 328 GLN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 657 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.142884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.106092 restraints weight = 20950.043| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.90 r_work: 0.3330 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2508 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= 0.157 Angle : 0.573 9.217 15840 Z= 0.310 Chirality : 0.041 0.169 1734 Planarity : 0.004 0.042 1958 Dihedral : 8.154 58.868 1596 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 6.15 % Allowed : 15.05 % 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 aren not related in a simple way. whole: 0.69 (0.22), residues: 1346 helix: 1.49 (0.17), residues: 814 sheet: -0.29 (0.59), residues: 64 loop : -1.29 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 354 TYR 0.015 0.001 TYR A 323 PHE 0.018 0.001 PHE A 556 TRP 0.016 0.001 TRP B 463 HIS 0.002 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00329 (11674) covalent geometry : angle 0.57276 (15828) SS BOND : bond 0.00281 ( 6) SS BOND : angle 0.65630 ( 12) hydrogen bonds : bond 0.05923 ( 715) hydrogen bonds : angle 5.03080 ( 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 215 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 139 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.7408 (m-80) REVERT: A 142 MET cc_start: 0.5091 (mmm) cc_final: 0.3836 (mtp) REVERT: A 370 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7671 (mtmt) REVERT: A 405 GLU cc_start: 0.8450 (tt0) cc_final: 0.7784 (tp30) REVERT: A 524 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7650 (pp) REVERT: A 530 LYS cc_start: 0.8976 (mmtm) cc_final: 0.8667 (mtpt) REVERT: A 534 MET cc_start: 0.8326 (tmm) cc_final: 0.8060 (tmm) REVERT: A 548 GLU cc_start: 0.8257 (pt0) cc_final: 0.8012 (pt0) REVERT: A 613 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7495 (mmt) REVERT: A 726 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8529 (tt0) REVERT: A 788 ASP cc_start: 0.6966 (OUTLIER) cc_final: 0.6000 (t0) REVERT: A 812 PHE cc_start: 0.8261 (m-80) cc_final: 0.7954 (m-80) REVERT: A 852 PHE cc_start: 0.8112 (m-10) cc_final: 0.7887 (m-10) REVERT: A 855 TYR cc_start: 0.8219 (t80) cc_final: 0.7840 (t80) REVERT: A 862 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6788 (pmtt) REVERT: B 73 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7127 (m-80) REVERT: B 93 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8322 (ptmm) REVERT: B 216 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7698 (mp) REVERT: B 286 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8105 (p0) REVERT: B 290 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8507 (pptt) REVERT: B 363 ILE cc_start: 0.7348 (OUTLIER) cc_final: 0.6940 (pt) REVERT: B 365 CYS cc_start: 0.7125 (OUTLIER) cc_final: 0.6595 (t) REVERT: B 395 GLU cc_start: 0.8726 (mp0) cc_final: 0.8397 (mp0) REVERT: B 409 ASP cc_start: 0.8654 (m-30) cc_final: 0.7500 (t0) REVERT: B 524 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7999 (pp) REVERT: B 530 LYS cc_start: 0.8232 (mmtm) cc_final: 0.7493 (tmtt) REVERT: B 534 MET cc_start: 0.7389 (mmt) cc_final: 0.6723 (ttm) REVERT: B 654 TYR cc_start: 0.7247 (t80) cc_final: 0.6851 (t80) REVERT: B 730 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.7755 (mp-120) REVERT: B 750 MET cc_start: 0.8864 (ttm) cc_final: 0.8135 (tpt) REVERT: B 773 MET cc_start: 0.8811 (mmt) cc_final: 0.8316 (tpt) REVERT: B 843 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8646 (mt-10) REVERT: B 855 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7288 (t80) outliers start: 76 outliers final: 27 residues processed: 201 average time/residue: 0.3976 time to fit residues: 88.9122 Evaluate side-chains 164 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 120 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 370 LYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 524 LEU 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 613 MET Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 726 GLN 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 216 ILE 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 7 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.141511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.104429 restraints weight = 21133.572| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.95 r_work: 0.3304 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2765 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= 0.187 Angle : 0.582 9.245 15840 Z= 0.313 Chirality : 0.042 0.191 1734 Planarity : 0.004 0.043 1958 Dihedral : 7.222 57.798 1573 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 5.91 % Allowed : 15.78 % Favored : 78.32 % 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 aren not related in a simple way. whole: 0.65 (0.22), residues: 1346 helix: 1.52 (0.17), residues: 802 sheet: -0.46 (0.59), residues: 64 loop : -1.33 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 354 TYR 0.014 0.001 TYR A 580 PHE 0.038 0.002 PHE A 558 TRP 0.028 0.001 TRP B 463 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00408 (11674) covalent geometry : angle 0.58246 (15828) SS BOND : bond 0.00318 ( 6) SS BOND : angle 0.57251 ( 12) hydrogen bonds : bond 0.06020 ( 715) hydrogen bonds : angle 5.00591 ( 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 205 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 132 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.7546 (m-80) REVERT: A 290 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8512 (tmmt) REVERT: A 365 CYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7792 (t) REVERT: A 370 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7771 (mtmt) REVERT: A 530 LYS cc_start: 0.8947 (mmtm) cc_final: 0.8610 (mtpt) REVERT: A 534 MET cc_start: 0.8372 (tmm) cc_final: 0.8107 (tmm) REVERT: A 788 ASP cc_start: 0.7054 (OUTLIER) cc_final: 0.6254 (t0) REVERT: A 855 TYR cc_start: 0.8238 (t80) cc_final: 0.7883 (t80) REVERT: A 862 LYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6769 (pmtt) REVERT: B 73 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7269 (m-80) REVERT: B 93 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8323 (ptmm) REVERT: B 271 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.6818 (tpm-80) REVERT: B 286 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8115 (p0) REVERT: B 290 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8501 (pptt) REVERT: B 322 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7884 (tm) REVERT: B 363 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.7013 (mp) REVERT: B 365 CYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6628 (t) REVERT: B 395 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8404 (mp0) REVERT: B 409 ASP cc_start: 0.8622 (m-30) cc_final: 0.7407 (t0) REVERT: B 524 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8018 (pp) REVERT: B 525 ASN cc_start: 0.8576 (m-40) cc_final: 0.7592 (m110) REVERT: B 530 LYS cc_start: 0.8307 (mmtm) cc_final: 0.7490 (tmtt) REVERT: B 534 MET cc_start: 0.7296 (mmt) cc_final: 0.6662 (ttm) REVERT: B 542 ARG cc_start: 0.5026 (OUTLIER) cc_final: 0.4222 (ttm110) REVERT: B 580 TYR cc_start: 0.8116 (p90) cc_final: 0.7851 (p90) REVERT: B 750 MET cc_start: 0.8919 (ttm) cc_final: 0.8210 (tpt) REVERT: B 773 MET cc_start: 0.8720 (mmt) cc_final: 0.8247 (tpt) REVERT: B 843 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8640 (mt-10) REVERT: B 855 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.7279 (t80) outliers start: 73 outliers final: 32 residues processed: 193 average time/residue: 0.4198 time to fit residues: 89.9696 Evaluate side-chains 173 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 123 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 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 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 543 THR Chi-restraints excluded: chain A residue 561 VAL 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 862 LYS 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 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 591 TYR Chi-restraints excluded: chain B residue 611 ILE 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 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: 2.9990 chunk 134 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 110 optimal weight: 0.0050 chunk 103 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.143289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.106629 restraints weight = 20792.690| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.91 r_work: 0.3336 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3025 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= 0.150 Angle : 0.570 9.237 15840 Z= 0.304 Chirality : 0.041 0.163 1734 Planarity : 0.004 0.041 1958 Dihedral : 7.111 58.656 1570 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.94 % Allowed : 17.39 % Favored : 77.67 % 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 aren not related in a simple way. whole: 0.70 (0.22), residues: 1346 helix: 1.54 (0.17), residues: 814 sheet: -0.44 (0.59), residues: 64 loop : -1.34 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 810 TYR 0.020 0.001 TYR A 528 PHE 0.038 0.001 PHE A 558 TRP 0.032 0.001 TRP B 463 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00313 (11674) covalent geometry : angle 0.57012 (15828) SS BOND : bond 0.00269 ( 6) SS BOND : angle 0.51115 ( 12) hydrogen bonds : bond 0.05710 ( 715) hydrogen bonds : angle 4.94106 ( 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 198 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 137 time to evaluate : 0.312 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: 0.8777 (OUTLIER) cc_final: 0.7397 (m-80) REVERT: A 290 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.9011 (ttmt) REVERT: A 365 CYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7724 (t) REVERT: A 370 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7727 (mtmt) REVERT: A 472 ILE cc_start: 0.7422 (mt) cc_final: 0.7199 (pt) REVERT: A 534 MET cc_start: 0.8429 (tmm) cc_final: 0.8127 (tmm) REVERT: A 788 ASP cc_start: 0.6916 (OUTLIER) cc_final: 0.6270 (t0) REVERT: B 73 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.7071 (m-80) REVERT: B 93 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8311 (ptmm) REVERT: B 216 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7700 (mp) REVERT: B 271 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.6723 (tpm-80) REVERT: B 286 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8112 (p0) REVERT: B 290 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8501 (pptt) REVERT: B 322 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7870 (tm) REVERT: B 329 ASP cc_start: 0.8237 (p0) cc_final: 0.7962 (p0) REVERT: B 363 ILE cc_start: 0.7356 (OUTLIER) cc_final: 0.6942 (pt) REVERT: B 365 CYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6581 (t) REVERT: B 395 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8441 (mp0) REVERT: B 409 ASP cc_start: 0.8601 (m-30) cc_final: 0.7339 (t0) REVERT: B 521 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.9041 (tt) REVERT: B 524 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8082 (pp) REVERT: B 525 ASN cc_start: 0.8451 (m-40) cc_final: 0.8010 (m110) REVERT: B 534 MET cc_start: 0.7280 (mmt) cc_final: 0.6488 (ttm) REVERT: B 542 ARG cc_start: 0.4803 (OUTLIER) cc_final: 0.4103 (ttm170) REVERT: B 654 TYR cc_start: 0.7215 (t80) cc_final: 0.6929 (t80) REVERT: B 750 MET cc_start: 0.8891 (ttm) cc_final: 0.8178 (tpt) REVERT: B 773 MET cc_start: 0.8760 (mmt) cc_final: 0.8247 (tpt) REVERT: B 788 ASP cc_start: 0.5852 (OUTLIER) cc_final: 0.4625 (t0) REVERT: B 843 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8631 (mt-10) REVERT: B 855 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.7239 (t80) outliers start: 61 outliers final: 26 residues processed: 189 average time/residue: 0.4002 time to fit residues: 84.6245 Evaluate side-chains 171 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 125 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 288 ILE Chi-restraints excluded: chain A residue 290 LYS 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 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 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 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 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: 4.9990 chunk 23 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 HIS ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.139715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.104743 restraints weight = 21018.866| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.88 r_work: 0.3273 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11680 Z= 0.245 Angle : 0.642 10.212 15840 Z= 0.342 Chirality : 0.044 0.173 1734 Planarity : 0.005 0.043 1958 Dihedral : 7.054 58.447 1562 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 6.23 % Allowed : 17.07 % Favored : 76.70 % 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 aren not related in a simple way. whole: 0.46 (0.22), residues: 1346 helix: 1.37 (0.17), residues: 816 sheet: 0.14 (0.64), residues: 44 loop : -1.55 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 478 TYR 0.020 0.002 TYR A 586 PHE 0.034 0.002 PHE A 558 TRP 0.021 0.001 TRP B 463 HIS 0.009 0.001 HIS A 518 Details of bonding type rmsd covalent geometry : bond 0.00549 (11674) covalent geometry : angle 0.64221 (15828) SS BOND : bond 0.00387 ( 6) SS BOND : angle 0.59869 ( 12) hydrogen bonds : bond 0.06268 ( 715) hydrogen bonds : angle 5.09102 ( 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 208 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 131 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.7688 (m-80) REVERT: A 365 CYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7851 (t) REVERT: A 370 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7779 (mtmt) REVERT: A 534 MET cc_start: 0.8451 (tmm) cc_final: 0.8119 (tmm) REVERT: A 548 GLU cc_start: 0.8282 (pt0) cc_final: 0.8071 (pt0) REVERT: A 726 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8580 (tt0) REVERT: A 855 TYR cc_start: 0.8237 (t80) cc_final: 0.7907 (t80) REVERT: B 73 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7209 (m-80) REVERT: B 93 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8318 (ptmm) REVERT: B 142 MET cc_start: 0.6949 (mtm) cc_final: 0.6407 (pmm) REVERT: B 271 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.6735 (tpm-80) REVERT: B 286 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8113 (p0) REVERT: B 290 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8490 (pptt) REVERT: B 322 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7891 (tm) REVERT: B 329 ASP cc_start: 0.8304 (p0) cc_final: 0.8030 (p0) REVERT: B 352 CYS cc_start: 0.7875 (t) cc_final: 0.7187 (p) REVERT: B 365 CYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6715 (t) REVERT: B 395 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8424 (mp0) REVERT: B 409 ASP cc_start: 0.8673 (m-30) cc_final: 0.7334 (t0) REVERT: B 528 TYR cc_start: 0.7789 (OUTLIER) cc_final: 0.7463 (m-80) REVERT: B 534 MET cc_start: 0.7353 (mmt) cc_final: 0.6658 (ttm) REVERT: B 542 ARG cc_start: 0.4934 (OUTLIER) cc_final: 0.4300 (ttm170) REVERT: B 654 TYR cc_start: 0.7445 (t80) cc_final: 0.7225 (t80) REVERT: B 750 MET cc_start: 0.8932 (ttm) cc_final: 0.8200 (tpt) REVERT: B 773 MET cc_start: 0.8554 (mmt) cc_final: 0.8197 (tpt) REVERT: B 788 ASP cc_start: 0.6192 (OUTLIER) cc_final: 0.4884 (t0) REVERT: B 843 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8668 (mt-10) REVERT: B 855 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.7290 (t80) outliers start: 77 outliers final: 31 residues processed: 194 average time/residue: 0.4323 time to fit residues: 93.1931 Evaluate side-chains 166 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 119 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 288 ILE Chi-restraints excluded: chain A residue 315 VAL 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 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 46 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 120 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 HIS ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.142481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.106600 restraints weight = 21086.393| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.82 r_work: 0.3364 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11680 Z= 0.163 Angle : 0.614 10.976 15840 Z= 0.323 Chirality : 0.042 0.211 1734 Planarity : 0.004 0.042 1958 Dihedral : 6.919 56.420 1560 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.61 % Allowed : 18.37 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.22), residues: 1346 helix: 1.45 (0.17), residues: 816 sheet: 0.14 (0.65), 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 0.029 0.001 TYR B 77 PHE 0.035 0.002 PHE A 558 TRP 0.036 0.001 TRP B 463 HIS 0.015 0.001 HIS A 518 Details of bonding type rmsd covalent geometry : bond 0.00348 (11674) covalent geometry : angle 0.61383 (15828) SS BOND : bond 0.00302 ( 6) SS BOND : angle 0.54269 ( 12) hydrogen bonds : bond 0.05853 ( 715) hydrogen bonds : angle 5.01852 ( 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 188 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 131 time to evaluate : 0.397 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: 0.8898 (OUTLIER) cc_final: 0.7529 (m-80) REVERT: A 365 CYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7840 (t) REVERT: A 370 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7891 (mtmt) REVERT: A 534 MET cc_start: 0.8429 (tmm) cc_final: 0.8089 (tmm) REVERT: A 548 GLU cc_start: 0.8280 (pt0) cc_final: 0.8024 (pt0) REVERT: A 788 ASP cc_start: 0.6701 (m-30) cc_final: 0.6231 (t0) REVERT: A 855 TYR cc_start: 0.8180 (t80) cc_final: 0.7861 (t80) REVERT: B 73 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7226 (m-80) REVERT: B 93 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8325 (ptmm) REVERT: B 286 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8234 (p0) REVERT: B 290 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8508 (pptt) REVERT: B 322 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8016 (tm) REVERT: B 329 ASP cc_start: 0.8208 (p0) cc_final: 0.7982 (p0) REVERT: B 363 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7096 (mp) REVERT: B 365 CYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6612 (t) REVERT: B 395 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8420 (mp0) REVERT: B 409 ASP cc_start: 0.8600 (m-30) cc_final: 0.7312 (t0) REVERT: B 534 MET cc_start: 0.7356 (mmt) cc_final: 0.6663 (ttm) REVERT: B 750 MET cc_start: 0.8907 (ttm) cc_final: 0.8310 (tpt) REVERT: B 773 MET cc_start: 0.8716 (mmt) cc_final: 0.8167 (tpt) REVERT: B 788 ASP cc_start: 0.5507 (OUTLIER) cc_final: 0.5222 (t0) REVERT: B 843 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8677 (mt-10) REVERT: B 855 TYR cc_start: 0.8094 (OUTLIER) cc_final: 0.7178 (t80) outliers start: 57 outliers final: 23 residues processed: 178 average time/residue: 0.3968 time to fit residues: 79.0712 Evaluate side-chains 163 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 543 THR Chi-restraints excluded: chain A residue 561 VAL 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 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 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 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: 3.9990 chunk 18 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 HIS ** 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 = 0.4026 r_free = 0.4026 target = 0.142034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.105970 restraints weight = 20851.411| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.82 r_work: 0.3373 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3406 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= 0.172 Angle : 0.625 15.799 15840 Z= 0.328 Chirality : 0.042 0.197 1734 Planarity : 0.004 0.042 1958 Dihedral : 6.694 56.934 1558 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.77 % Allowed : 18.37 % Favored : 76.86 % 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 aren not related in a simple way. whole: 0.60 (0.22), residues: 1346 helix: 1.47 (0.17), residues: 816 sheet: 0.06 (0.64), residues: 44 loop : -1.46 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 478 TYR 0.025 0.002 TYR B 77 PHE 0.035 0.002 PHE B 558 TRP 0.025 0.001 TRP B 463 HIS 0.021 0.001 HIS A 518 Details of bonding type rmsd covalent geometry : bond 0.00372 (11674) covalent geometry : angle 0.62538 (15828) SS BOND : bond 0.00289 ( 6) SS BOND : angle 0.47924 ( 12) hydrogen bonds : bond 0.05912 ( 715) hydrogen bonds : angle 5.02442 ( 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 196 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 137 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.7596 (m-80) REVERT: A 271 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8210 (tpp-160) REVERT: A 365 CYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7900 (t) REVERT: A 370 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7957 (mtmt) REVERT: A 534 MET cc_start: 0.8405 (tmm) cc_final: 0.7971 (tmm) REVERT: A 548 GLU cc_start: 0.8307 (pt0) cc_final: 0.8024 (pt0) REVERT: A 788 ASP cc_start: 0.6656 (m-30) cc_final: 0.6293 (t0) REVERT: B 73 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7126 (m-80) REVERT: B 93 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8332 (ptmm) REVERT: B 271 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.6849 (tpm-80) REVERT: B 286 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8262 (p0) REVERT: B 290 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8546 (pptt) REVERT: B 322 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8041 (tm) REVERT: B 363 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7177 (mp) REVERT: B 365 CYS cc_start: 0.7041 (OUTLIER) cc_final: 0.6693 (t) REVERT: B 395 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8412 (mp0) REVERT: B 409 ASP cc_start: 0.8581 (m-30) cc_final: 0.7350 (t0) REVERT: B 534 MET cc_start: 0.7341 (mmt) cc_final: 0.6687 (ttm) REVERT: B 542 ARG cc_start: 0.4849 (OUTLIER) cc_final: 0.4309 (ttm110) REVERT: B 750 MET cc_start: 0.8944 (ttm) cc_final: 0.8365 (tpt) REVERT: B 760 PHE cc_start: 0.7799 (m-80) cc_final: 0.7403 (m-10) REVERT: B 773 MET cc_start: 0.8665 (mmt) cc_final: 0.8117 (tpt) REVERT: B 827 TYR cc_start: 0.7452 (t80) cc_final: 0.7225 (t80) REVERT: B 855 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.7146 (t80) outliers start: 59 outliers final: 27 residues processed: 182 average time/residue: 0.4188 time to fit residues: 84.9552 Evaluate side-chains 168 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 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 411 VAL 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 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 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 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 611 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 34 optimal weight: 20.0000 chunk 98 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 108 optimal weight: 0.0470 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 HIS ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4033 r_free = 0.4033 target = 0.142538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.106858 restraints weight = 20681.863| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.80 r_work: 0.3372 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11680 Z= 0.161 Angle : 0.652 19.179 15840 Z= 0.338 Chirality : 0.043 0.199 1734 Planarity : 0.004 0.041 1958 Dihedral : 6.556 57.217 1556 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.64 % Allowed : 20.15 % Favored : 76.21 % 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 aren not related in a simple way. whole: 0.64 (0.22), residues: 1346 helix: 1.48 (0.17), residues: 816 sheet: 0.11 (0.65), residues: 44 loop : -1.41 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 478 TYR 0.022 0.001 TYR A 827 PHE 0.047 0.002 PHE B 558 TRP 0.020 0.001 TRP B 463 HIS 0.024 0.001 HIS A 518 Details of bonding type rmsd covalent geometry : bond 0.00342 (11674) covalent geometry : angle 0.65196 (15828) SS BOND : bond 0.00256 ( 6) SS BOND : angle 0.50306 ( 12) hydrogen bonds : bond 0.05848 ( 715) hydrogen bonds : angle 5.01271 ( 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 177 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 132 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.7478 (m-80) REVERT: A 365 CYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7818 (t) REVERT: A 370 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7867 (mtmt) REVERT: A 381 ILE cc_start: 0.8982 (mt) cc_final: 0.8741 (mt) REVERT: A 534 MET cc_start: 0.8403 (tmm) cc_final: 0.7998 (tmm) REVERT: A 548 GLU cc_start: 0.8324 (pt0) cc_final: 0.8089 (pt0) REVERT: A 558 PHE cc_start: 0.7584 (m-80) cc_final: 0.7292 (t80) REVERT: A 788 ASP cc_start: 0.6539 (m-30) cc_final: 0.6283 (t0) REVERT: B 93 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8334 (ptmm) REVERT: B 286 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8224 (p0) REVERT: B 290 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8517 (pptt) REVERT: B 322 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8014 (tm) REVERT: B 363 ILE cc_start: 0.7500 (OUTLIER) cc_final: 0.6919 (mp) REVERT: B 395 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8426 (mp0) REVERT: B 409 ASP cc_start: 0.8566 (m-30) cc_final: 0.7352 (t0) REVERT: B 534 MET cc_start: 0.7318 (mmt) cc_final: 0.6656 (ttm) REVERT: B 750 MET cc_start: 0.8948 (ttm) cc_final: 0.8283 (tpt) REVERT: B 760 PHE cc_start: 0.7757 (m-80) cc_final: 0.7326 (m-10) REVERT: B 773 MET cc_start: 0.8692 (mmt) cc_final: 0.8115 (tpt) REVERT: B 827 TYR cc_start: 0.7455 (t80) cc_final: 0.7220 (t80) REVERT: B 855 TYR cc_start: 0.8099 (OUTLIER) cc_final: 0.7141 (t80) REVERT: B 867 LYS cc_start: 0.9022 (mtmt) cc_final: 0.8630 (mmtt) outliers start: 45 outliers final: 25 residues processed: 163 average time/residue: 0.4073 time to fit residues: 74.6138 Evaluate side-chains 161 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 543 THR 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 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 395 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 521 ILE 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 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: 0.9990 chunk 13 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 131 optimal weight: 4.9990 chunk 92 optimal weight: 0.0370 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 = 0.4041 r_free = 0.4041 target = 0.143237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.107425 restraints weight = 20733.939| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.82 r_work: 0.3384 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11680 Z= 0.155 Angle : 0.654 18.500 15840 Z= 0.341 Chirality : 0.043 0.200 1734 Planarity : 0.005 0.041 1958 Dihedral : 6.296 55.898 1551 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.64 % Allowed : 20.79 % Favored : 75.57 % 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 aren not related in a simple way. whole: 0.65 (0.22), residues: 1346 helix: 1.50 (0.17), residues: 816 sheet: 0.14 (0.66), residues: 44 loop : -1.41 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 478 TYR 0.019 0.001 TYR B 325 PHE 0.040 0.002 PHE B 558 TRP 0.047 0.001 TRP B 463 HIS 0.028 0.001 HIS A 518 Details of bonding type rmsd covalent geometry : bond 0.00326 (11674) covalent geometry : angle 0.65373 (15828) SS BOND : bond 0.00266 ( 6) SS BOND : angle 0.46189 ( 12) hydrogen bonds : bond 0.05763 ( 715) hydrogen bonds : angle 4.99796 ( 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 177 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 132 time to evaluate : 0.475 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: 0.8924 (OUTLIER) cc_final: 0.7460 (m-80) REVERT: A 271 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8210 (tpp-160) REVERT: A 365 CYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7832 (t) REVERT: A 370 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7839 (mtmt) REVERT: A 381 ILE cc_start: 0.8974 (mt) cc_final: 0.8727 (mt) REVERT: A 534 MET cc_start: 0.8383 (tmm) cc_final: 0.7974 (tmm) REVERT: A 548 GLU cc_start: 0.8334 (pt0) cc_final: 0.8102 (pt0) REVERT: B 93 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8319 (ptmm) REVERT: B 271 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.6770 (tpm-80) REVERT: B 286 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8235 (p0) REVERT: B 290 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8512 (pptt) REVERT: B 322 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8019 (tm) REVERT: B 365 CYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6619 (t) REVERT: B 395 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8413 (mp0) REVERT: B 534 MET cc_start: 0.7307 (mmt) cc_final: 0.6647 (ttm) REVERT: B 542 ARG cc_start: 0.4731 (OUTLIER) cc_final: 0.4412 (ttm110) REVERT: B 750 MET cc_start: 0.8938 (ttm) cc_final: 0.8308 (tpt) REVERT: B 760 PHE cc_start: 0.7678 (m-80) cc_final: 0.7285 (m-10) REVERT: B 827 TYR cc_start: 0.7440 (t80) cc_final: 0.7194 (t80) REVERT: B 855 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.7113 (t80) REVERT: B 867 LYS cc_start: 0.8998 (mtmt) cc_final: 0.8610 (mmtt) outliers start: 45 outliers final: 24 residues processed: 167 average time/residue: 0.4569 time to fit residues: 85.0429 Evaluate side-chains 163 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 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 543 THR 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 93 LYS 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 521 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 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: 2.9990 chunk 38 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 HIS ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.140752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.104677 restraints weight = 20973.994| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.80 r_work: 0.3337 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11680 Z= 0.219 Angle : 0.700 20.488 15840 Z= 0.366 Chirality : 0.045 0.232 1734 Planarity : 0.005 0.069 1958 Dihedral : 6.400 55.860 1551 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.40 % Allowed : 21.20 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.22), residues: 1346 helix: 1.39 (0.17), residues: 816 sheet: -0.18 (0.66), residues: 44 loop : -1.53 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 69 TYR 0.020 0.002 TYR B 325 PHE 0.041 0.002 PHE B 558 TRP 0.046 0.002 TRP B 463 HIS 0.026 0.002 HIS A 518 Details of bonding type rmsd covalent geometry : bond 0.00489 (11674) covalent geometry : angle 0.69996 (15828) SS BOND : bond 0.00366 ( 6) SS BOND : angle 0.53718 ( 12) hydrogen bonds : bond 0.06188 ( 715) hydrogen bonds : angle 5.11000 ( 2109) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3695.06 seconds wall clock time: 64 minutes 0.07 seconds (3840.07 seconds total)