Starting phenix.real_space_refine on Wed May 14 05:18:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b8q_15919/05_2025/8b8q_15919.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b8q_15919/05_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_15919/05_2025/8b8q_15919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b8q_15919/05_2025/8b8q_15919.map" model { file = "/net/cci-nas-00/data/ceres_data/8b8q_15919/05_2025/8b8q_15919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b8q_15919/05_2025/8b8q_15919.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.45, per 1000 atoms: 0.83 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: 2.91 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.14 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: 4.03 Time building geometry restraints manager: 3.39 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: 0.06 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: 11.590 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: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 31.700 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 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:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.050 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.018 0.001 TRP A 397 HIS 0.003 0.001 HIS A 249 PHE 0.014 0.001 PHE A 556 TYR 0.014 0.001 TYR A 580 ARG 0.003 0.000 ARG B 813 Details of bonding type rmsd hydrogen bonds : bond 0.13280 ( 715) hydrogen bonds : angle 5.66342 ( 2109) SS BOND : bond 0.00287 ( 6) SS BOND : angle 0.66812 ( 12) covalent geometry : bond 0.00384 (11674) covalent geometry : angle 0.54234 (15828) *********************** 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 : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.7988 (m-80) REVERT: A 272 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7744 (tm-30) REVERT: A 327 ASP cc_start: 0.8159 (m-30) cc_final: 0.7950 (m-30) REVERT: A 365 CYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7790 (t) REVERT: A 370 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7823 (mtmt) REVERT: A 472 ILE cc_start: 0.7612 (mt) cc_final: 0.7398 (pt) REVERT: A 530 LYS cc_start: 0.8992 (mmtm) cc_final: 0.8646 (mtmt) REVERT: A 534 MET cc_start: 0.8316 (mmt) cc_final: 0.7972 (tmm) REVERT: A 588 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6255 (pp) REVERT: A 613 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7548 (mmt) REVERT: A 772 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8331 (p) REVERT: A 785 ASN cc_start: 0.5675 (OUTLIER) cc_final: 0.5425 (p0) REVERT: A 855 TYR cc_start: 0.8258 (t80) cc_final: 0.7672 (t80) REVERT: A 862 LYS cc_start: 0.7175 (OUTLIER) cc_final: 0.6830 (pmtt) REVERT: B 93 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8355 (ptpt) REVERT: B 271 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7278 (mmm160) REVERT: B 290 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8382 (pptt) REVERT: B 295 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7716 (mtpt) REVERT: B 352 CYS cc_start: 0.7732 (t) cc_final: 0.6759 (p) REVERT: B 365 CYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6662 (t) REVERT: B 395 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8328 (mp0) REVERT: B 409 ASP cc_start: 0.8661 (m-30) cc_final: 0.7602 (t0) REVERT: B 524 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8006 (pp) REVERT: B 534 MET cc_start: 0.7440 (mmt) cc_final: 0.6687 (ttm) REVERT: B 657 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7451 (mm-40) REVERT: B 714 MET cc_start: 0.8245 (mtm) cc_final: 0.7704 (mpm) REVERT: B 750 MET cc_start: 0.8771 (ttm) cc_final: 0.8055 (tpt) REVERT: B 773 MET cc_start: 0.8830 (mmt) cc_final: 0.8464 (tpt) REVERT: B 788 ASP cc_start: 0.6648 (OUTLIER) cc_final: 0.3723 (t0) REVERT: B 843 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8661 (mt-10) outliers start: 98 outliers final: 24 residues processed: 296 average time/residue: 1.1809 time to fit residues: 378.4552 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 : 1.325 ------------------------------------------------------------------------------- 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 116 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.0570 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 108 optimal weight: 0.0670 chunk 41 optimal weight: 0.1980 chunk 65 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 125 optimal weight: 0.9980 overall best weight: 0.3036 ------------------------------------------------------------------------------- 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 544 GLN A 785 ASN B 108 HIS ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 GLN B 544 GLN B 674 GLN B 695 ASN B 710 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.145432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.111045 restraints weight = 20648.051| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.87 r_work: 0.3382 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2238 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= 0.143 Angle : 0.586 9.555 15840 Z= 0.314 Chirality : 0.041 0.138 1734 Planarity : 0.005 0.039 1958 Dihedral : 8.311 59.992 1607 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.83 % Allowed : 14.24 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.23), residues: 1346 helix: 1.69 (0.17), residues: 814 sheet: 0.17 (0.60), residues: 64 loop : -1.20 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 397 HIS 0.002 0.001 HIS B 108 PHE 0.017 0.001 PHE A 556 TYR 0.016 0.001 TYR A 323 ARG 0.007 0.000 ARG B 810 Details of bonding type rmsd hydrogen bonds : bond 0.05786 ( 715) hydrogen bonds : angle 5.01114 ( 2109) SS BOND : bond 0.00288 ( 6) SS BOND : angle 0.95401 ( 12) covalent geometry : bond 0.00292 (11674) covalent geometry : angle 0.58593 (15828) *********************** 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 223 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 151 time to evaluate : 1.194 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: 0.8727 (OUTLIER) cc_final: 0.7412 (m-80) REVERT: A 142 MET cc_start: 0.4866 (mmm) cc_final: 0.3554 (mtp) REVERT: A 234 ASN cc_start: 0.9357 (t0) cc_final: 0.9153 (p0) REVERT: A 328 GLN cc_start: 0.7937 (tt0) cc_final: 0.7700 (tt0) REVERT: A 370 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7668 (mtmt) REVERT: A 463 TRP cc_start: 0.7786 (t-100) cc_final: 0.7323 (t-100) REVERT: A 472 ILE cc_start: 0.7313 (mt) cc_final: 0.7079 (pt) REVERT: A 548 GLU cc_start: 0.8145 (pt0) cc_final: 0.7903 (pt0) REVERT: A 613 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7425 (mmt) REVERT: A 812 PHE cc_start: 0.8008 (m-80) cc_final: 0.7628 (m-80) REVERT: A 855 TYR cc_start: 0.8205 (t80) cc_final: 0.7807 (t80) REVERT: A 862 LYS cc_start: 0.7284 (OUTLIER) cc_final: 0.6860 (pmtt) REVERT: B 73 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7129 (m-80) REVERT: B 93 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8300 (ptpt) REVERT: B 216 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7471 (mp) REVERT: B 271 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7620 (mmm160) REVERT: B 286 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8117 (p0) REVERT: B 290 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8487 (pptt) REVERT: B 322 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7861 (tm) REVERT: B 365 CYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6570 (t) REVERT: B 395 GLU cc_start: 0.8731 (mp0) cc_final: 0.8328 (mp0) REVERT: B 409 ASP cc_start: 0.8550 (m-30) cc_final: 0.7493 (t0) REVERT: B 524 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7995 (pp) REVERT: B 525 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.7914 (m110) REVERT: B 534 MET cc_start: 0.7286 (mmt) cc_final: 0.6441 (ttm) REVERT: B 594 GLU cc_start: 0.8399 (pt0) cc_final: 0.7660 (pm20) REVERT: B 654 TYR cc_start: 0.7119 (t80) cc_final: 0.6869 (t80) REVERT: B 730 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8516 (mp10) REVERT: B 750 MET cc_start: 0.8816 (ttm) cc_final: 0.8065 (tpt) REVERT: B 773 MET cc_start: 0.8855 (mmt) cc_final: 0.8425 (tpt) REVERT: B 843 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8609 (mt-10) REVERT: B 855 TYR cc_start: 0.8051 (OUTLIER) cc_final: 0.7240 (t80) outliers start: 72 outliers final: 28 residues processed: 204 average time/residue: 0.9119 time to fit residues: 206.7875 Evaluate side-chains 168 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 124 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 216 ILE 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 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 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 783 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 832 ILE 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 56 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 84 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 GLN B 695 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.142666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.107883 restraints weight = 21057.978| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.89 r_work: 0.3334 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11680 Z= 0.186 Angle : 0.584 9.265 15840 Z= 0.315 Chirality : 0.042 0.166 1734 Planarity : 0.004 0.040 1958 Dihedral : 7.698 58.681 1582 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 6.96 % Allowed : 14.81 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.23), residues: 1346 helix: 1.58 (0.17), residues: 814 sheet: -0.17 (0.60), residues: 64 loop : -1.28 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 463 HIS 0.003 0.001 HIS B 249 PHE 0.018 0.001 PHE A 556 TYR 0.014 0.001 TYR A 528 ARG 0.008 0.000 ARG B 354 Details of bonding type rmsd hydrogen bonds : bond 0.05976 ( 715) hydrogen bonds : angle 4.99793 ( 2109) SS BOND : bond 0.00294 ( 6) SS BOND : angle 0.63518 ( 12) covalent geometry : bond 0.00407 (11674) covalent geometry : angle 0.58441 (15828) *********************** 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 218 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 132 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.7554 (m-80) REVERT: A 328 GLN cc_start: 0.8084 (tt0) cc_final: 0.7834 (tt0) REVERT: A 365 CYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7798 (t) REVERT: A 369 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7674 (mtmm) REVERT: A 370 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7742 (mtmt) REVERT: A 472 ILE cc_start: 0.7429 (mt) cc_final: 0.7190 (pt) REVERT: A 534 MET cc_start: 0.8344 (tmm) cc_final: 0.8121 (tmm) REVERT: A 548 GLU cc_start: 0.8225 (pt0) cc_final: 0.7985 (pt0) REVERT: A 613 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7424 (mmt) REVERT: A 812 PHE cc_start: 0.8263 (m-80) cc_final: 0.7798 (m-80) REVERT: B 93 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8318 (ptmm) REVERT: B 216 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7577 (mp) REVERT: B 286 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8380 (t0) REVERT: B 290 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8417 (pptt) REVERT: B 365 CYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6700 (t) REVERT: B 395 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8402 (mp0) REVERT: B 409 ASP cc_start: 0.8583 (m-30) cc_final: 0.7467 (t0) REVERT: B 524 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8017 (pp) REVERT: B 530 LYS cc_start: 0.8445 (mmtm) cc_final: 0.7578 (tmtt) REVERT: B 533 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8228 (pp) REVERT: B 534 MET cc_start: 0.7435 (mmt) cc_final: 0.6658 (ttm) REVERT: B 594 GLU cc_start: 0.8419 (pt0) cc_final: 0.7644 (pm20) REVERT: B 654 TYR cc_start: 0.7232 (t80) cc_final: 0.6996 (t80) REVERT: B 750 MET cc_start: 0.8867 (ttm) cc_final: 0.8145 (tpt) REVERT: B 773 MET cc_start: 0.8678 (mmt) cc_final: 0.8187 (tpt) REVERT: B 843 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8640 (mt-10) REVERT: B 855 TYR cc_start: 0.8088 (OUTLIER) cc_final: 0.7252 (t80) outliers start: 86 outliers final: 34 residues processed: 203 average time/residue: 0.9955 time to fit residues: 225.1009 Evaluate side-chains 166 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 118 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 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 370 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 533 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 43 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 37 optimal weight: 0.0060 chunk 132 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 99 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 GLN 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 = 0.142882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.107783 restraints weight = 20989.158| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.84 r_work: 0.3337 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2692 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 : 0.579 9.308 15840 Z= 0.310 Chirality : 0.041 0.177 1734 Planarity : 0.004 0.040 1958 Dihedral : 7.253 57.293 1570 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 6.39 % Allowed : 15.53 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.22), residues: 1346 helix: 1.57 (0.17), residues: 814 sheet: -0.29 (0.60), residues: 64 loop : -1.29 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 463 HIS 0.003 0.001 HIS A 249 PHE 0.018 0.001 PHE A 556 TYR 0.016 0.001 TYR A 528 ARG 0.010 0.000 ARG B 69 Details of bonding type rmsd hydrogen bonds : bond 0.05863 ( 715) hydrogen bonds : angle 4.96858 ( 2109) SS BOND : bond 0.00307 ( 6) SS BOND : angle 0.56348 ( 12) covalent geometry : bond 0.00373 (11674) covalent geometry : angle 0.57899 (15828) *********************** 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 212 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 133 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.7540 (m-80) REVERT: A 264 SER cc_start: 0.8659 (OUTLIER) cc_final: 0.8438 (m) REVERT: A 365 CYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7763 (t) REVERT: A 369 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7676 (mtmm) REVERT: A 370 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7741 (mtmt) REVERT: A 534 MET cc_start: 0.8372 (tmm) cc_final: 0.8043 (tmm) REVERT: A 613 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7417 (mmt) REVERT: A 812 PHE cc_start: 0.8272 (m-80) cc_final: 0.8037 (m-80) REVERT: B 93 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8315 (ptmm) REVERT: B 216 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7669 (mp) REVERT: B 271 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.6779 (tpm-80) REVERT: B 286 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8113 (p0) REVERT: B 290 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8474 (pptt) REVERT: B 329 ASP cc_start: 0.8259 (p0) cc_final: 0.7975 (p0) REVERT: B 365 CYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6702 (t) REVERT: B 395 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8420 (mp0) REVERT: B 409 ASP cc_start: 0.8591 (m-30) cc_final: 0.7395 (t0) REVERT: B 524 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7975 (pp) REVERT: B 534 MET cc_start: 0.7304 (mmt) cc_final: 0.6573 (ttt) REVERT: B 580 TYR cc_start: 0.8038 (OUTLIER) cc_final: 0.7780 (p90) REVERT: B 654 TYR cc_start: 0.7320 (t80) cc_final: 0.6920 (t80) REVERT: B 750 MET cc_start: 0.8872 (ttm) cc_final: 0.8139 (tpt) REVERT: B 773 MET cc_start: 0.8676 (mmt) cc_final: 0.8166 (tpt) REVERT: B 843 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8629 (mt-10) REVERT: B 855 TYR cc_start: 0.8110 (OUTLIER) cc_final: 0.7265 (t80) outliers start: 79 outliers final: 35 residues processed: 197 average time/residue: 0.8693 time to fit residues: 191.2928 Evaluate side-chains 174 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 123 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 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 759 SER Chi-restraints excluded: chain A residue 780 THR 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 525 ASN Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 580 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 0.0370 chunk 111 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 133 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN B 674 GLN B 695 ASN B 726 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.143248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.108461 restraints weight = 20771.816| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.91 r_work: 0.3333 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11680 Z= 0.164 Angle : 0.578 9.661 15840 Z= 0.308 Chirality : 0.041 0.160 1734 Planarity : 0.004 0.041 1958 Dihedral : 7.006 59.224 1566 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.58 % Allowed : 16.83 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.22), residues: 1346 helix: 1.56 (0.17), residues: 816 sheet: -0.38 (0.59), residues: 64 loop : -1.27 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 463 HIS 0.003 0.001 HIS A 249 PHE 0.041 0.002 PHE A 558 TYR 0.018 0.001 TYR A 528 ARG 0.006 0.000 ARG B 69 Details of bonding type rmsd hydrogen bonds : bond 0.05786 ( 715) hydrogen bonds : angle 4.92814 ( 2109) SS BOND : bond 0.00300 ( 6) SS BOND : angle 1.61446 ( 12) covalent geometry : bond 0.00350 (11674) covalent geometry : angle 0.57662 (15828) *********************** 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 200 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 131 time to evaluate : 1.333 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: 0.8754 (OUTLIER) cc_final: 0.7455 (m-80) REVERT: A 264 SER cc_start: 0.8672 (OUTLIER) cc_final: 0.8442 (m) REVERT: A 290 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8505 (tmmt) REVERT: A 365 CYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7731 (t) REVERT: A 369 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7685 (mtmm) REVERT: A 370 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7765 (mtmt) REVERT: A 534 MET cc_start: 0.8427 (tmm) cc_final: 0.8133 (tmm) REVERT: A 613 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7394 (mmt) REVERT: B 73 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.6431 (m-80) REVERT: B 93 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8304 (ptmm) REVERT: B 271 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.6753 (tpm-80) REVERT: B 286 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8109 (p0) REVERT: B 290 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8494 (pptt) REVERT: B 322 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7872 (tm) REVERT: B 365 CYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6640 (t) REVERT: B 395 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8440 (mp0) REVERT: B 409 ASP cc_start: 0.8592 (m-30) cc_final: 0.7365 (t0) REVERT: B 524 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8039 (pp) REVERT: B 525 ASN cc_start: 0.8370 (m-40) cc_final: 0.8158 (m110) REVERT: B 534 MET cc_start: 0.7298 (mmt) cc_final: 0.6596 (ttt) REVERT: B 542 ARG cc_start: 0.4763 (OUTLIER) cc_final: 0.3927 (ttm170) REVERT: B 580 TYR cc_start: 0.8041 (p90) cc_final: 0.7789 (p90) REVERT: B 654 TYR cc_start: 0.7443 (t80) cc_final: 0.7199 (t80) REVERT: B 750 MET cc_start: 0.8900 (ttm) cc_final: 0.8188 (tpt) REVERT: B 773 MET cc_start: 0.8668 (mmt) cc_final: 0.8110 (tpt) REVERT: B 788 ASP cc_start: 0.5840 (OUTLIER) cc_final: 0.4265 (t0) REVERT: B 843 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8630 (mt-10) REVERT: B 855 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.7252 (t80) outliers start: 69 outliers final: 34 residues processed: 188 average time/residue: 0.8901 time to fit residues: 186.3696 Evaluate side-chains 175 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 122 time to evaluate : 1.317 ------------------------------------------------------------------------------- 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 264 SER Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 535 ILE 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 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 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 780 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 855 TYR Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 559 GLN B 674 GLN B 695 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.142755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.108143 restraints weight = 21136.568| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.89 r_work: 0.3340 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11680 Z= 0.170 Angle : 0.591 9.674 15840 Z= 0.315 Chirality : 0.042 0.175 1734 Planarity : 0.004 0.041 1958 Dihedral : 6.838 55.354 1564 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 5.91 % Allowed : 16.99 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.22), residues: 1346 helix: 1.53 (0.17), residues: 818 sheet: 0.42 (0.65), residues: 44 loop : -1.37 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 463 HIS 0.003 0.001 HIS A 249 PHE 0.031 0.002 PHE A 558 TYR 0.016 0.001 TYR B 827 ARG 0.004 0.000 ARG A 478 Details of bonding type rmsd hydrogen bonds : bond 0.05806 ( 715) hydrogen bonds : angle 4.93144 ( 2109) SS BOND : bond 0.00305 ( 6) SS BOND : angle 1.22137 ( 12) covalent geometry : bond 0.00368 (11674) covalent geometry : angle 0.59050 (15828) *********************** 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 199 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 126 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.7597 (m-80) REVERT: A 290 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.9026 (ttmt) REVERT: A 365 CYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7742 (t) REVERT: A 369 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7678 (mtmm) REVERT: A 370 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7784 (mtmt) REVERT: A 534 MET cc_start: 0.8465 (tmm) cc_final: 0.8066 (tmm) REVERT: A 613 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7404 (mmt) REVERT: B 93 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8301 (ptmm) REVERT: B 142 MET cc_start: 0.6858 (mtm) cc_final: 0.6565 (ptp) REVERT: B 286 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8116 (p0) REVERT: B 290 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8455 (pptt) REVERT: B 322 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7906 (tm) REVERT: B 365 CYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6666 (t) REVERT: B 395 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8435 (mp0) REVERT: B 409 ASP cc_start: 0.8587 (m-30) cc_final: 0.7332 (t0) REVERT: B 524 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8070 (pp) REVERT: B 534 MET cc_start: 0.7309 (mmt) cc_final: 0.6614 (ttt) REVERT: B 580 TYR cc_start: 0.8065 (p90) cc_final: 0.7816 (p90) REVERT: B 750 MET cc_start: 0.8897 (ttm) cc_final: 0.8171 (tpt) REVERT: B 773 MET cc_start: 0.8607 (mmt) cc_final: 0.8050 (tpt) REVERT: B 788 ASP cc_start: 0.5891 (OUTLIER) cc_final: 0.4692 (t0) REVERT: B 843 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8632 (mt-10) REVERT: B 855 TYR cc_start: 0.8150 (OUTLIER) cc_final: 0.7271 (t80) outliers start: 73 outliers final: 36 residues processed: 183 average time/residue: 0.8376 time to fit residues: 171.7905 Evaluate side-chains 168 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 117 time to evaluate : 1.300 ------------------------------------------------------------------------------- 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 264 SER 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 369 LYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 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 613 MET Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 372 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 525 ASN Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 855 TYR Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 20 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 559 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.142271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.106068 restraints weight = 21263.320| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.81 r_work: 0.3383 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3179 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= 0.196 Angle : 0.616 11.747 15840 Z= 0.329 Chirality : 0.043 0.200 1734 Planarity : 0.004 0.041 1958 Dihedral : 6.881 56.281 1562 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.66 % Allowed : 17.56 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.22), residues: 1346 helix: 1.45 (0.17), residues: 818 sheet: 0.20 (0.66), residues: 44 loop : -1.38 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 463 HIS 0.004 0.001 HIS A 275 PHE 0.037 0.002 PHE A 558 TYR 0.019 0.001 TYR A 827 ARG 0.004 0.000 ARG A 813 Details of bonding type rmsd hydrogen bonds : bond 0.06027 ( 715) hydrogen bonds : angle 5.00418 ( 2109) SS BOND : bond 0.00350 ( 6) SS BOND : angle 1.14565 ( 12) covalent geometry : bond 0.00431 (11674) covalent geometry : angle 0.61557 (15828) *********************** 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 193 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 123 time to evaluate : 1.311 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: 0.8931 (OUTLIER) cc_final: 0.7843 (m-80) REVERT: A 271 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8125 (tpp-160) REVERT: A 365 CYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7962 (t) REVERT: A 370 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7989 (mtmt) REVERT: A 534 MET cc_start: 0.8454 (tmm) cc_final: 0.8045 (tmm) REVERT: A 613 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7546 (mmt) REVERT: B 93 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8310 (ptmm) REVERT: B 142 MET cc_start: 0.7083 (mtm) cc_final: 0.6850 (ptp) REVERT: B 286 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8241 (p0) REVERT: B 290 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8544 (pptt) REVERT: B 322 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8059 (tm) REVERT: B 365 CYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6743 (t) REVERT: B 395 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8393 (mp0) REVERT: B 409 ASP cc_start: 0.8587 (m-30) cc_final: 0.7331 (t0) REVERT: B 534 MET cc_start: 0.7364 (mmt) cc_final: 0.6704 (ttt) REVERT: B 542 ARG cc_start: 0.4687 (OUTLIER) cc_final: 0.3988 (ttm170) REVERT: B 654 TYR cc_start: 0.7314 (t80) cc_final: 0.7071 (t80) REVERT: B 657 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7555 (mt0) REVERT: B 750 MET cc_start: 0.8930 (ttm) cc_final: 0.8371 (tpt) REVERT: B 760 PHE cc_start: 0.7894 (m-80) cc_final: 0.7432 (m-10) REVERT: B 773 MET cc_start: 0.8602 (mmt) cc_final: 0.8155 (tpt) REVERT: B 788 ASP cc_start: 0.5826 (OUTLIER) cc_final: 0.4883 (OUTLIER) REVERT: B 855 TYR cc_start: 0.8107 (OUTLIER) cc_final: 0.7218 (t80) outliers start: 70 outliers final: 34 residues processed: 181 average time/residue: 0.8618 time to fit residues: 174.4832 Evaluate side-chains 162 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 115 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 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 759 SER Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 372 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 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 780 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 855 TYR Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 127 optimal weight: 0.0980 chunk 88 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.142912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.107005 restraints weight = 21064.886| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.82 r_work: 0.3378 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11680 Z= 0.164 Angle : 0.617 12.024 15840 Z= 0.325 Chirality : 0.043 0.196 1734 Planarity : 0.004 0.041 1958 Dihedral : 6.526 56.493 1557 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.77 % Allowed : 18.69 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.22), residues: 1346 helix: 1.51 (0.17), residues: 818 sheet: 0.21 (0.65), residues: 44 loop : -1.37 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 463 HIS 0.007 0.001 HIS A 275 PHE 0.029 0.002 PHE A 558 TYR 0.058 0.001 TYR B 528 ARG 0.006 0.000 ARG A 478 Details of bonding type rmsd hydrogen bonds : bond 0.05828 ( 715) hydrogen bonds : angle 4.96585 ( 2109) SS BOND : bond 0.00280 ( 6) SS BOND : angle 0.99426 ( 12) covalent geometry : bond 0.00351 (11674) covalent geometry : angle 0.61657 (15828) *********************** 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 191 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 132 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.7679 (m-80) REVERT: A 365 CYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7864 (t) REVERT: A 370 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7909 (mtmt) REVERT: A 381 ILE cc_start: 0.8982 (mt) cc_final: 0.8732 (mt) REVERT: A 534 MET cc_start: 0.8461 (tmm) cc_final: 0.8043 (tmm) REVERT: A 613 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7580 (mmt) REVERT: A 788 ASP cc_start: 0.6623 (m-30) cc_final: 0.6201 (t0) REVERT: B 93 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8321 (ptmm) REVERT: B 271 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.6786 (tpm-80) REVERT: B 286 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8225 (p0) REVERT: B 290 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8508 (pptt) REVERT: B 322 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8032 (tm) REVERT: B 365 CYS cc_start: 0.7118 (OUTLIER) cc_final: 0.6675 (t) REVERT: B 395 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8430 (mp0) REVERT: B 409 ASP cc_start: 0.8570 (m-30) cc_final: 0.7343 (t0) REVERT: B 534 MET cc_start: 0.7322 (mmt) cc_final: 0.6662 (ttt) REVERT: B 542 ARG cc_start: 0.4662 (OUTLIER) cc_final: 0.4129 (ttm110) REVERT: B 654 TYR cc_start: 0.7410 (t80) cc_final: 0.7209 (t80) REVERT: B 657 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7539 (mt0) REVERT: B 750 MET cc_start: 0.8915 (ttm) cc_final: 0.8318 (tpt) REVERT: B 773 MET cc_start: 0.8665 (mmt) cc_final: 0.8266 (tpt) REVERT: B 827 TYR cc_start: 0.7516 (t80) cc_final: 0.6873 (m-80) REVERT: B 855 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.7204 (t80) outliers start: 59 outliers final: 31 residues processed: 180 average time/residue: 0.8917 time to fit residues: 180.5957 Evaluate side-chains 165 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 121 time to evaluate : 1.357 ------------------------------------------------------------------------------- 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 264 SER 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 613 MET 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 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 372 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 542 ARG Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 855 TYR Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 37 optimal weight: 0.0040 chunk 136 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 559 GLN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 GLN B 695 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.144002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.108380 restraints weight = 20952.301| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.81 r_work: 0.3406 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11680 Z= 0.156 Angle : 0.627 12.731 15840 Z= 0.332 Chirality : 0.042 0.198 1734 Planarity : 0.005 0.047 1958 Dihedral : 6.533 59.698 1557 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.45 % Allowed : 19.82 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.22), residues: 1346 helix: 1.55 (0.18), residues: 806 sheet: 0.14 (0.66), residues: 44 loop : -1.33 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP B 463 HIS 0.007 0.001 HIS A 275 PHE 0.031 0.001 PHE B 558 TYR 0.024 0.001 TYR A 827 ARG 0.003 0.000 ARG A 478 Details of bonding type rmsd hydrogen bonds : bond 0.05826 ( 715) hydrogen bonds : angle 4.97562 ( 2109) SS BOND : bond 0.00246 ( 6) SS BOND : angle 0.90710 ( 12) covalent geometry : bond 0.00327 (11674) covalent geometry : angle 0.62692 (15828) *********************** 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 188 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 133 time to evaluate : 1.282 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: 0.8961 (OUTLIER) cc_final: 0.7611 (m-80) REVERT: A 365 CYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7870 (t) REVERT: A 370 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7908 (mtmt) REVERT: A 381 ILE cc_start: 0.8989 (mt) cc_final: 0.8734 (mt) REVERT: A 534 MET cc_start: 0.8423 (tmm) cc_final: 0.7987 (tmm) REVERT: A 613 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7544 (mmt) REVERT: A 788 ASP cc_start: 0.6472 (m-30) cc_final: 0.6219 (t0) REVERT: B 93 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8318 (ptmm) REVERT: B 216 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7925 (mp) REVERT: B 271 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.6807 (tpm-80) REVERT: B 286 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8248 (p0) REVERT: B 290 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8527 (pptt) REVERT: B 322 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8040 (tm) REVERT: B 365 CYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6675 (t) REVERT: B 395 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8431 (mp0) REVERT: B 409 ASP cc_start: 0.8553 (m-30) cc_final: 0.7346 (t0) REVERT: B 534 MET cc_start: 0.7281 (mmt) cc_final: 0.6664 (ttt) REVERT: B 542 ARG cc_start: 0.4549 (OUTLIER) cc_final: 0.4103 (ttm110) REVERT: B 750 MET cc_start: 0.8901 (ttm) cc_final: 0.8339 (tpt) REVERT: B 773 MET cc_start: 0.8679 (mmt) cc_final: 0.8154 (tpt) REVERT: B 827 TYR cc_start: 0.7271 (t80) cc_final: 0.6895 (m-80) REVERT: B 855 TYR cc_start: 0.8068 (OUTLIER) cc_final: 0.7120 (t80) outliers start: 55 outliers final: 26 residues processed: 179 average time/residue: 0.8506 time to fit residues: 170.4561 Evaluate side-chains 161 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 264 SER 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 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 613 MET 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 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 364 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 372 CYS 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 521 ILE Chi-restraints excluded: chain B residue 526 THR 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 47 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 674 GLN B 695 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.142884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.108531 restraints weight = 20890.677| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.88 r_work: 0.3368 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11680 Z= 0.177 Angle : 0.656 13.078 15840 Z= 0.348 Chirality : 0.043 0.198 1734 Planarity : 0.005 0.041 1958 Dihedral : 6.524 58.131 1555 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.48 % Allowed : 21.04 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.22), residues: 1346 helix: 1.48 (0.17), residues: 818 sheet: 0.01 (0.67), residues: 44 loop : -1.34 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.097 0.002 TRP B 463 HIS 0.007 0.001 HIS A 275 PHE 0.031 0.002 PHE A 556 TYR 0.026 0.001 TYR A 827 ARG 0.003 0.000 ARG B 69 Details of bonding type rmsd hydrogen bonds : bond 0.05982 ( 715) hydrogen bonds : angle 5.01412 ( 2109) SS BOND : bond 0.00295 ( 6) SS BOND : angle 0.95158 ( 12) covalent geometry : bond 0.00383 (11674) covalent geometry : angle 0.65595 (15828) ********************** 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 167 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 124 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.7637 (m-80) REVERT: A 142 MET cc_start: 0.4092 (mmp) cc_final: 0.3453 (mtm) REVERT: A 365 CYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7860 (t) REVERT: A 370 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7944 (mtmt) REVERT: A 534 MET cc_start: 0.8459 (tmm) cc_final: 0.8041 (tmm) REVERT: A 613 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7525 (mmt) REVERT: A 657 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7230 (tm-30) REVERT: A 788 ASP cc_start: 0.6571 (m-30) cc_final: 0.6315 (t0) REVERT: B 53 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7993 (pm20) REVERT: B 93 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8308 (ptmm) REVERT: B 286 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8218 (p0) REVERT: B 290 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8513 (pptt) REVERT: B 322 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8035 (tm) REVERT: B 329 ASP cc_start: 0.8130 (p0) cc_final: 0.7922 (p0) REVERT: B 363 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7583 (pt) REVERT: B 365 CYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6808 (t) REVERT: B 395 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8437 (mp0) REVERT: B 409 ASP cc_start: 0.8544 (m-30) cc_final: 0.7347 (t0) REVERT: B 534 MET cc_start: 0.7280 (mmt) cc_final: 0.6675 (ttt) REVERT: B 542 ARG cc_start: 0.4521 (OUTLIER) cc_final: 0.4034 (ttm170) REVERT: B 750 MET cc_start: 0.8962 (ttm) cc_final: 0.8304 (tpt) REVERT: B 773 MET cc_start: 0.8646 (mmt) cc_final: 0.8221 (tpt) REVERT: B 827 TYR cc_start: 0.7333 (t80) cc_final: 0.6873 (m-80) REVERT: B 855 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.7163 (t80) REVERT: B 867 LYS cc_start: 0.9014 (mtpt) cc_final: 0.8633 (mmtt) outliers start: 43 outliers final: 23 residues processed: 159 average time/residue: 0.8994 time to fit residues: 159.4755 Evaluate side-chains 156 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 264 SER 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 613 MET Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 53 GLU 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 474 ILE Chi-restraints excluded: chain B residue 521 ILE 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 67 optimal weight: 0.0170 chunk 92 optimal weight: 0.7980 chunk 54 optimal weight: 0.0040 chunk 81 optimal weight: 0.0870 chunk 34 optimal weight: 10.0000 chunk 51 optimal weight: 0.0670 chunk 62 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 57 optimal weight: 0.0000 chunk 105 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.0350 ------------------------------------------------------------------------------- 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 674 GLN A 695 ASN ** 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 = 0.4093 r_free = 0.4093 target = 0.148022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.112650 restraints weight = 20942.860| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.84 r_work: 0.3475 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4058 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= 0.137 Angle : 0.636 14.110 15840 Z= 0.336 Chirality : 0.042 0.242 1734 Planarity : 0.005 0.044 1958 Dihedral : 6.346 58.124 1555 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.83 % Allowed : 21.68 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.23), residues: 1346 helix: 1.53 (0.17), residues: 826 sheet: 0.26 (0.68), residues: 44 loop : -1.15 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 463 HIS 0.005 0.001 HIS A 275 PHE 0.035 0.001 PHE B 558 TYR 0.031 0.001 TYR B 77 ARG 0.007 0.000 ARG A 478 Details of bonding type rmsd hydrogen bonds : bond 0.05443 ( 715) hydrogen bonds : angle 4.90258 ( 2109) SS BOND : bond 0.00185 ( 6) SS BOND : angle 0.83211 ( 12) covalent geometry : bond 0.00267 (11674) covalent geometry : angle 0.63587 (15828) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7401.57 seconds wall clock time: 129 minutes 6.17 seconds (7746.17 seconds total)