Starting phenix.real_space_refine on Tue Feb 3 21:12:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y48_72474/02_2026/9y48_72474.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y48_72474/02_2026/9y48_72474.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y48_72474/02_2026/9y48_72474.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y48_72474/02_2026/9y48_72474.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y48_72474/02_2026/9y48_72474.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y48_72474/02_2026/9y48_72474.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.038 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 S 29 5.16 5 Na 1 4.78 5 C 4367 2.51 5 N 1142 2.21 5 O 1292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6831 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 875, 6830 Classifications: {'peptide': 875} Link IDs: {'PCIS': 5, 'PTRANS': 38, 'TRANS': 831} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.23, per 1000 atoms: 0.18 Number of scatterers: 6831 At special positions: 0 Unit cell: (69.204, 81.468, 120.888, 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) S 29 16.00 Na 1 11.00 O 1292 8.00 N 1142 7.00 C 4367 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 232.4 milliseconds 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1640 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 14 sheets defined 9.9% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 380 through 390 Processing helix chain 'A' and resid 449 through 453 removed outlier: 3.645A pdb=" N PHE A 453 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 460 removed outlier: 3.727A pdb=" N TRP A 459 " --> pdb=" O ASN A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 483 removed outlier: 4.561A pdb=" N GLY A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA A 483 " --> pdb=" O GLY A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 544 Processing helix chain 'A' and resid 614 through 617 removed outlier: 3.570A pdb=" N ALA A 617 " --> pdb=" O ARG A 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 614 through 617' Processing helix chain 'A' and resid 723 through 725 No H-bonds generated for 'chain 'A' and resid 723 through 725' Processing helix chain 'A' and resid 760 through 766 Processing helix chain 'A' and resid 767 through 770 Processing helix chain 'A' and resid 860 through 864 removed outlier: 3.580A pdb=" N GLU A 863 " --> pdb=" O TYR A 860 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER A 864 " --> pdb=" O ILE A 861 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 860 through 864' Processing helix chain 'A' and resid 926 through 936 Processing helix chain 'A' and resid 944 through 950 removed outlier: 4.440A pdb=" N ILE A 948 " --> pdb=" O TYR A 944 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 75 removed outlier: 6.729A pdb=" N LEU A 883 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS A 73 " --> pdb=" O ALA A 881 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA A 881 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 86 removed outlier: 6.526A pdb=" N ALA A 95 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA A 83 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA A 93 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHE A 85 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 91 " --> pdb=" O PHE A 85 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLU A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 127 removed outlier: 6.928A pdb=" N ILE A 135 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N MET A 124 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 133 " --> pdb=" O MET A 124 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE A 126 " --> pdb=" O TYR A 131 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR A 131 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N THR A 140 " --> pdb=" O ASN A 136 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A 141 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR A 154 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL A 143 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 161 through 166 removed outlier: 3.731A pdb=" N SER A 163 " --> pdb=" O GLY A 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 216 through 219 removed outlier: 6.759A pdb=" N THR A 235 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER A 248 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR A 237 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 274 through 279 removed outlier: 6.916A pdb=" N ILE A 289 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER A 277 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE A 287 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TYR A 279 " --> pdb=" O HIS A 285 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N HIS A 285 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASP A 299 " --> pdb=" O MET A 305 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N MET A 305 " --> pdb=" O ASP A 299 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 334 through 341 removed outlier: 6.665A pdb=" N SER A 353 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL A 337 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A 351 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TRP A 339 " --> pdb=" O SER A 349 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N SER A 349 " --> pdb=" O TRP A 339 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N CYS A 341 " --> pdb=" O TYR A 347 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N TYR A 347 " --> pdb=" O CYS A 341 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N THR A 348 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 405 through 411 removed outlier: 4.383A pdb=" N LEU A 426 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR A 438 " --> pdb=" O THR A 447 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 464 through 473 removed outlier: 4.071A pdb=" N SER A 518 " --> pdb=" O HIS A 514 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 551 through 557 removed outlier: 3.969A pdb=" N THR A 629 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LYS A 576 " --> pdb=" O PRO A 627 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU A 578 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N PHE A 625 " --> pdb=" O GLU A 578 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 638 through 643 removed outlier: 3.853A pdb=" N SER A 657 " --> pdb=" O TYR A 653 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU A 658 " --> pdb=" O MET A 671 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET A 671 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU A 660 " --> pdb=" O ILE A 669 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 685 through 694 removed outlier: 3.629A pdb=" N CYS A 687 " --> pdb=" O GLY A 708 " (cutoff:3.500A) removed outlier: 13.874A pdb=" N SER A 701 " --> pdb=" O PRO A 721 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE A 703 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU A 713 " --> pdb=" O THR A 709 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LYS A 718 " --> pdb=" O LEU A 731 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU A 731 " --> pdb=" O LYS A 718 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU A 720 " --> pdb=" O VAL A 729 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL A 729 " --> pdb=" O LEU A 720 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 745 through 750 removed outlier: 4.430A pdb=" N LYS A 745 " --> pdb=" O THR A 780 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 804 through 815 removed outlier: 3.669A pdb=" N GLY A 808 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N HIS A 835 " --> pdb=" O GLU A 831 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU A 836 " --> pdb=" O SER A 849 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER A 849 " --> pdb=" O LEU A 836 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL A 838 " --> pdb=" O GLN A 847 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 549 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.79 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: 2199 1.34 - 1.46: 1450 1.46 - 1.58: 3273 1.58 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 6972 Sorted by residual: bond pdb=" CA ASN A 423 " pdb=" CB ASN A 423 " ideal model delta sigma weight residual 1.522 1.531 -0.009 7.00e-03 2.04e+04 1.49e+00 bond pdb=" CB ASN A 516 " pdb=" CG ASN A 516 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.44e+00 bond pdb=" CA MET A 626 " pdb=" CB MET A 626 " ideal model delta sigma weight residual 1.535 1.519 0.016 1.42e-02 4.96e+03 1.27e+00 bond pdb=" C VAL A 613 " pdb=" O VAL A 613 " ideal model delta sigma weight residual 1.236 1.225 0.012 1.19e-02 7.06e+03 9.56e-01 bond pdb=" CB GLU A 291 " pdb=" CG GLU A 291 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.76e-01 ... (remaining 6967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 9274 1.99 - 3.97: 164 3.97 - 5.96: 19 5.96 - 7.94: 3 7.94 - 9.93: 2 Bond angle restraints: 9462 Sorted by residual: angle pdb=" C MET A 732 " pdb=" N ASP A 733 " pdb=" CA ASP A 733 " ideal model delta sigma weight residual 121.80 112.97 8.83 1.71e+00 3.42e-01 2.66e+01 angle pdb=" C SER A 358 " pdb=" CA SER A 358 " pdb=" CB SER A 358 " ideal model delta sigma weight residual 116.63 111.18 5.45 1.16e+00 7.43e-01 2.21e+01 angle pdb=" CB MET A 848 " pdb=" CG MET A 848 " pdb=" SD MET A 848 " ideal model delta sigma weight residual 112.70 102.77 9.93 3.00e+00 1.11e-01 1.10e+01 angle pdb=" C ILE A 164 " pdb=" N ASP A 165 " pdb=" CA ASP A 165 " ideal model delta sigma weight residual 122.37 116.83 5.54 1.72e+00 3.38e-01 1.04e+01 angle pdb=" CA MET A 848 " pdb=" CB MET A 848 " pdb=" CG MET A 848 " ideal model delta sigma weight residual 114.10 120.50 -6.40 2.00e+00 2.50e-01 1.02e+01 ... (remaining 9457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3759 17.95 - 35.89: 342 35.89 - 53.84: 83 53.84 - 71.79: 23 71.79 - 89.73: 9 Dihedral angle restraints: 4216 sinusoidal: 1666 harmonic: 2550 Sorted by residual: dihedral pdb=" CA GLU A 123 " pdb=" C GLU A 123 " pdb=" N MET A 124 " pdb=" CA MET A 124 " ideal model delta harmonic sigma weight residual 180.00 161.80 18.20 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA MET A 848 " pdb=" C MET A 848 " pdb=" N SER A 849 " pdb=" CA SER A 849 " ideal model delta harmonic sigma weight residual 180.00 162.25 17.75 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ASN A 516 " pdb=" C ASN A 516 " pdb=" N GLY A 517 " pdb=" CA GLY A 517 " ideal model delta harmonic sigma weight residual -180.00 -162.99 -17.01 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 4213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 683 0.034 - 0.068: 257 0.068 - 0.102: 92 0.102 - 0.136: 54 0.136 - 0.170: 5 Chirality restraints: 1091 Sorted by residual: chirality pdb=" CA ILE A 743 " pdb=" N ILE A 743 " pdb=" C ILE A 743 " pdb=" CB ILE A 743 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.26e-01 chirality pdb=" CA ILE A 779 " pdb=" N ILE A 779 " pdb=" C ILE A 779 " pdb=" CB ILE A 779 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CG LEU A 933 " pdb=" CB LEU A 933 " pdb=" CD1 LEU A 933 " pdb=" CD2 LEU A 933 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.42e-01 ... (remaining 1088 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 461 " -0.052 5.00e-02 4.00e+02 7.88e-02 9.93e+00 pdb=" N PRO A 462 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 462 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 462 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 280 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO A 281 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 281 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 281 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 70 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" CD GLU A 70 " 0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU A 70 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A 70 " -0.011 2.00e-02 2.50e+03 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 98 2.67 - 3.22: 6191 3.22 - 3.78: 10401 3.78 - 4.34: 14433 4.34 - 4.90: 23745 Nonbonded interactions: 54868 Sorted by model distance: nonbonded pdb=" OG1 THR A 153 " pdb=" OH TYR A 944 " model vdw 2.108 3.040 nonbonded pdb=" OG SER A 566 " pdb=" OG1 THR A 638 " model vdw 2.133 3.040 nonbonded pdb=" OG SER A 193 " pdb=" O LEU A 934 " model vdw 2.146 3.040 nonbonded pdb=" OE1 GLU A 110 " pdb=" ND2 ASN A 456 " model vdw 2.175 3.120 nonbonded pdb=" O GLY A 870 " pdb=" OG1 THR A 886 " model vdw 2.191 3.040 ... (remaining 54863 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.530 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6018 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 : 0.003 0.036 6972 Z= 0.159 Angle : 0.688 9.930 9462 Z= 0.396 Chirality : 0.047 0.170 1091 Planarity : 0.005 0.079 1206 Dihedral : 15.779 89.733 2576 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.79 % Allowed : 16.40 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.28), residues: 871 helix: -0.61 (0.70), residues: 53 sheet: 0.23 (0.30), residues: 305 loop : -0.37 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 868 TYR 0.014 0.001 TYR A 717 PHE 0.016 0.002 PHE A 85 TRP 0.014 0.002 TRP A 477 HIS 0.003 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6972) covalent geometry : angle 0.68758 ( 9462) hydrogen bonds : bond 0.15793 ( 199) hydrogen bonds : angle 7.89070 ( 549) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.242 Fit side-chains REVERT: A 123 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7216 (tt0) REVERT: A 160 LYS cc_start: 0.7380 (tttt) cc_final: 0.6996 (mtmm) REVERT: A 435 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7525 (tt0) REVERT: A 437 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7193 (mt-10) REVERT: A 579 VAL cc_start: 0.6858 (t) cc_final: 0.6580 (m) REVERT: A 859 LYS cc_start: 0.7289 (tptt) cc_final: 0.7032 (mtmt) REVERT: A 929 GLN cc_start: 0.7073 (tm-30) cc_final: 0.6562 (tt0) outliers start: 6 outliers final: 3 residues processed: 111 average time/residue: 0.0820 time to fit residues: 12.1295 Evaluate side-chains 79 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 735 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0060 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 108 GLN A 136 ASN A 362 ASN A 390 ASN ** A 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.206746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.173416 restraints weight = 5904.084| |-----------------------------------------------------------------------------| r_work (start): 0.5522 rms_B_bonded: 2.11 r_work: 0.5265 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.5265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6972 Z= 0.124 Angle : 0.570 7.449 9462 Z= 0.299 Chirality : 0.048 0.227 1091 Planarity : 0.004 0.057 1206 Dihedral : 4.928 56.100 947 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.89 % Allowed : 14.57 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.29), residues: 871 helix: -0.10 (0.68), residues: 59 sheet: 0.04 (0.29), residues: 322 loop : -0.12 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 520 TYR 0.014 0.001 TYR A 695 PHE 0.013 0.001 PHE A 66 TRP 0.014 0.002 TRP A 298 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6972) covalent geometry : angle 0.57019 ( 9462) hydrogen bonds : bond 0.03790 ( 199) hydrogen bonds : angle 6.26855 ( 549) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.153 Fit side-chains REVERT: A 108 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6068 (mp10) REVERT: A 160 LYS cc_start: 0.7545 (tttt) cc_final: 0.7220 (mtmm) REVERT: A 342 GLU cc_start: 0.6400 (mt-10) cc_final: 0.6098 (mm-30) REVERT: A 347 TYR cc_start: 0.6358 (m-10) cc_final: 0.6059 (m-80) REVERT: A 579 VAL cc_start: 0.6645 (t) cc_final: 0.6399 (m) REVERT: A 672 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7402 (tt0) REVERT: A 859 LYS cc_start: 0.7288 (tptt) cc_final: 0.7065 (mtmt) REVERT: A 878 GLU cc_start: 0.7762 (mp0) cc_final: 0.7554 (mp0) REVERT: A 929 GLN cc_start: 0.7101 (tm-30) cc_final: 0.6862 (tt0) outliers start: 22 outliers final: 11 residues processed: 95 average time/residue: 0.0658 time to fit residues: 8.4771 Evaluate side-chains 85 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 826 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 83 optimal weight: 0.0370 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 422 HIS ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 GLN A 931 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.190739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.153876 restraints weight = 6123.778| |-----------------------------------------------------------------------------| r_work (start): 0.5321 rms_B_bonded: 2.24 r_work: 0.5095 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.5095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 6972 Z= 0.242 Angle : 0.702 7.314 9462 Z= 0.364 Chirality : 0.052 0.169 1091 Planarity : 0.006 0.062 1206 Dihedral : 5.471 56.121 946 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.07 % Allowed : 15.35 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.28), residues: 871 helix: -0.01 (0.71), residues: 59 sheet: -0.46 (0.28), residues: 316 loop : -0.50 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 461 TYR 0.019 0.002 TYR A 441 PHE 0.023 0.003 PHE A 66 TRP 0.019 0.003 TRP A 298 HIS 0.006 0.002 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00584 ( 6972) covalent geometry : angle 0.70168 ( 9462) hydrogen bonds : bond 0.04106 ( 199) hydrogen bonds : angle 6.61129 ( 549) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 0.263 Fit side-chains REVERT: A 128 LYS cc_start: 0.7189 (mmtp) cc_final: 0.6793 (mtmm) REVERT: A 160 LYS cc_start: 0.7511 (tttt) cc_final: 0.7150 (mtmm) REVERT: A 279 TYR cc_start: 0.6636 (OUTLIER) cc_final: 0.5647 (t80) REVERT: A 342 GLU cc_start: 0.6404 (mt-10) cc_final: 0.6180 (mm-30) REVERT: A 386 ASN cc_start: 0.5565 (t0) cc_final: 0.5195 (m-40) REVERT: A 439 MET cc_start: 0.7775 (ttm) cc_final: 0.7395 (ttp) REVERT: A 639 SER cc_start: 0.7932 (t) cc_final: 0.7711 (p) REVERT: A 859 LYS cc_start: 0.7454 (tptt) cc_final: 0.7180 (mtmt) REVERT: A 929 GLN cc_start: 0.7153 (tm-30) cc_final: 0.6774 (tt0) outliers start: 31 outliers final: 26 residues processed: 110 average time/residue: 0.0647 time to fit residues: 9.8502 Evaluate side-chains 105 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 889 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 19 optimal weight: 0.3980 chunk 49 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.191671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.154954 restraints weight = 6188.730| |-----------------------------------------------------------------------------| r_work (start): 0.5343 rms_B_bonded: 2.26 r_work: 0.5122 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.5122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6972 Z= 0.158 Angle : 0.578 6.716 9462 Z= 0.303 Chirality : 0.048 0.173 1091 Planarity : 0.005 0.068 1206 Dihedral : 5.075 59.123 945 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.12 % Allowed : 15.09 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.29), residues: 871 helix: 0.30 (0.75), residues: 59 sheet: -0.57 (0.29), residues: 310 loop : -0.46 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 520 TYR 0.015 0.001 TYR A 695 PHE 0.011 0.001 PHE A 535 TRP 0.019 0.002 TRP A 298 HIS 0.005 0.001 HIS A 632 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 6972) covalent geometry : angle 0.57771 ( 9462) hydrogen bonds : bond 0.03445 ( 199) hydrogen bonds : angle 6.21102 ( 549) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 76 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 128 LYS cc_start: 0.7212 (mmtp) cc_final: 0.6723 (mtmm) REVERT: A 160 LYS cc_start: 0.7479 (tttt) cc_final: 0.7145 (mtmm) REVERT: A 279 TYR cc_start: 0.6526 (OUTLIER) cc_final: 0.5608 (t80) REVERT: A 342 GLU cc_start: 0.6450 (mt-10) cc_final: 0.6191 (mm-30) REVERT: A 350 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6537 (mp) REVERT: A 386 ASN cc_start: 0.5495 (t0) cc_final: 0.5159 (m-40) REVERT: A 626 MET cc_start: 0.6211 (mtt) cc_final: 0.5871 (mtp) REVERT: A 859 LYS cc_start: 0.7402 (tptt) cc_final: 0.7103 (mtmt) outliers start: 39 outliers final: 26 residues processed: 103 average time/residue: 0.0692 time to fit residues: 9.8520 Evaluate side-chains 101 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 889 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.187830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.151617 restraints weight = 6348.096| |-----------------------------------------------------------------------------| r_work (start): 0.5300 rms_B_bonded: 2.22 r_work: 0.5076 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.5076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 6972 Z= 0.200 Angle : 0.635 9.129 9462 Z= 0.330 Chirality : 0.050 0.163 1091 Planarity : 0.006 0.062 1206 Dihedral : 5.234 55.027 945 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 6.17 % Allowed : 14.57 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.29), residues: 871 helix: 0.82 (0.78), residues: 53 sheet: -0.80 (0.28), residues: 322 loop : -0.49 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 868 TYR 0.015 0.002 TYR A 388 PHE 0.015 0.002 PHE A 87 TRP 0.018 0.002 TRP A 298 HIS 0.004 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 6972) covalent geometry : angle 0.63460 ( 9462) hydrogen bonds : bond 0.03588 ( 199) hydrogen bonds : angle 6.31302 ( 549) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 81 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 128 LYS cc_start: 0.7279 (mmtp) cc_final: 0.6779 (mtmm) REVERT: A 160 LYS cc_start: 0.7525 (tttt) cc_final: 0.7213 (mtmm) REVERT: A 279 TYR cc_start: 0.6611 (OUTLIER) cc_final: 0.5708 (t80) REVERT: A 340 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7486 (mpt) REVERT: A 342 GLU cc_start: 0.6422 (mt-10) cc_final: 0.6140 (mm-30) REVERT: A 350 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6630 (mp) REVERT: A 386 ASN cc_start: 0.5545 (t0) cc_final: 0.5186 (m-40) REVERT: A 439 MET cc_start: 0.7591 (ttm) cc_final: 0.7264 (ttp) REVERT: A 626 MET cc_start: 0.6340 (mtt) cc_final: 0.6002 (mtp) REVERT: A 859 LYS cc_start: 0.7505 (tptt) cc_final: 0.7258 (mtmt) outliers start: 47 outliers final: 37 residues processed: 113 average time/residue: 0.0627 time to fit residues: 9.9336 Evaluate side-chains 117 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 77 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 889 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 46 optimal weight: 0.2980 chunk 74 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 285 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.190410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.155639 restraints weight = 6251.631| |-----------------------------------------------------------------------------| r_work (start): 0.5345 rms_B_bonded: 2.23 r_work: 0.5103 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.5103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6972 Z= 0.148 Angle : 0.560 7.289 9462 Z= 0.292 Chirality : 0.048 0.156 1091 Planarity : 0.005 0.071 1206 Dihedral : 5.057 58.372 945 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.77 % Allowed : 16.40 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.29), residues: 871 helix: 0.48 (0.76), residues: 59 sheet: -0.74 (0.29), residues: 316 loop : -0.60 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 118 TYR 0.013 0.001 TYR A 717 PHE 0.010 0.001 PHE A 126 TRP 0.019 0.002 TRP A 298 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 6972) covalent geometry : angle 0.56029 ( 9462) hydrogen bonds : bond 0.03261 ( 199) hydrogen bonds : angle 6.05368 ( 549) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 82 time to evaluate : 0.157 Fit side-chains REVERT: A 128 LYS cc_start: 0.7257 (mmtp) cc_final: 0.6784 (mtmm) REVERT: A 160 LYS cc_start: 0.7640 (tttt) cc_final: 0.7309 (mtmm) REVERT: A 279 TYR cc_start: 0.6460 (OUTLIER) cc_final: 0.5702 (t80) REVERT: A 340 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7717 (mpt) REVERT: A 342 GLU cc_start: 0.6397 (mt-10) cc_final: 0.6174 (mm-30) REVERT: A 350 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6628 (mp) REVERT: A 386 ASN cc_start: 0.5594 (t0) cc_final: 0.5289 (m-40) REVERT: A 439 MET cc_start: 0.7510 (ttm) cc_final: 0.7224 (ttp) REVERT: A 626 MET cc_start: 0.6367 (mtt) cc_final: 0.6099 (mtp) REVERT: A 846 GLU cc_start: 0.6874 (tt0) cc_final: 0.6404 (mp0) REVERT: A 859 LYS cc_start: 0.7569 (tptt) cc_final: 0.7336 (mtmt) outliers start: 44 outliers final: 37 residues processed: 113 average time/residue: 0.0715 time to fit residues: 11.0843 Evaluate side-chains 119 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 79 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 876 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 66 optimal weight: 0.1980 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 0.0980 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.192272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.156062 restraints weight = 6145.368| |-----------------------------------------------------------------------------| r_work (start): 0.5356 rms_B_bonded: 2.25 r_work: 0.5142 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.5142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6972 Z= 0.117 Angle : 0.547 10.588 9462 Z= 0.283 Chirality : 0.048 0.273 1091 Planarity : 0.005 0.073 1206 Dihedral : 4.905 58.673 945 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 6.04 % Allowed : 16.27 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.29), residues: 871 helix: 0.57 (0.77), residues: 59 sheet: -0.65 (0.29), residues: 316 loop : -0.48 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 868 TYR 0.017 0.001 TYR A 695 PHE 0.010 0.001 PHE A 126 TRP 0.018 0.002 TRP A 298 HIS 0.004 0.001 HIS A 632 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 6972) covalent geometry : angle 0.54700 ( 9462) hydrogen bonds : bond 0.03079 ( 199) hydrogen bonds : angle 5.91842 ( 549) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 77 time to evaluate : 0.247 Fit side-chains REVERT: A 128 LYS cc_start: 0.7286 (mmtp) cc_final: 0.6688 (mtmm) REVERT: A 160 LYS cc_start: 0.7610 (tttt) cc_final: 0.7213 (mtmm) REVERT: A 279 TYR cc_start: 0.6512 (OUTLIER) cc_final: 0.5714 (t80) REVERT: A 342 GLU cc_start: 0.6530 (mt-10) cc_final: 0.6167 (mm-30) REVERT: A 350 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6655 (mp) REVERT: A 386 ASN cc_start: 0.5392 (t0) cc_final: 0.5114 (m-40) REVERT: A 439 MET cc_start: 0.7615 (ttm) cc_final: 0.7277 (ttp) REVERT: A 626 MET cc_start: 0.6251 (mtt) cc_final: 0.5992 (mtp) REVERT: A 776 ILE cc_start: 0.5852 (mm) cc_final: 0.5602 (mm) REVERT: A 846 GLU cc_start: 0.6911 (tt0) cc_final: 0.6310 (mp0) REVERT: A 859 LYS cc_start: 0.7482 (tptt) cc_final: 0.7221 (mtmt) outliers start: 46 outliers final: 37 residues processed: 112 average time/residue: 0.0606 time to fit residues: 9.7093 Evaluate side-chains 112 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 73 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 395 LYS Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 876 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 0.1980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 0.0980 chunk 23 optimal weight: 4.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.194755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.158302 restraints weight = 6180.131| |-----------------------------------------------------------------------------| r_work (start): 0.5359 rms_B_bonded: 2.26 r_work: 0.5150 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.5150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6972 Z= 0.119 Angle : 0.556 11.716 9462 Z= 0.289 Chirality : 0.048 0.230 1091 Planarity : 0.005 0.067 1206 Dihedral : 4.851 58.362 945 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.51 % Allowed : 17.06 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.29), residues: 871 helix: 0.60 (0.77), residues: 59 sheet: -0.63 (0.29), residues: 319 loop : -0.41 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 868 TYR 0.028 0.001 TYR A 695 PHE 0.009 0.001 PHE A 126 TRP 0.016 0.002 TRP A 298 HIS 0.003 0.001 HIS A 632 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 6972) covalent geometry : angle 0.55602 ( 9462) hydrogen bonds : bond 0.03111 ( 199) hydrogen bonds : angle 5.84889 ( 549) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 77 time to evaluate : 0.251 Fit side-chains REVERT: A 118 ARG cc_start: 0.5938 (mmm-85) cc_final: 0.5541 (mmm-85) REVERT: A 128 LYS cc_start: 0.7156 (mmtp) cc_final: 0.6607 (mtmm) REVERT: A 160 LYS cc_start: 0.7584 (tttt) cc_final: 0.7221 (mtmm) REVERT: A 279 TYR cc_start: 0.6563 (OUTLIER) cc_final: 0.5780 (t80) REVERT: A 340 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7536 (mpp) REVERT: A 342 GLU cc_start: 0.6561 (mt-10) cc_final: 0.6216 (mm-30) REVERT: A 386 ASN cc_start: 0.5390 (t0) cc_final: 0.5141 (m-40) REVERT: A 439 MET cc_start: 0.7525 (ttm) cc_final: 0.7201 (ttp) REVERT: A 626 MET cc_start: 0.6246 (mtt) cc_final: 0.6013 (mtp) REVERT: A 846 GLU cc_start: 0.6897 (tt0) cc_final: 0.6396 (mp0) REVERT: A 859 LYS cc_start: 0.7511 (tptt) cc_final: 0.7225 (mtmt) outliers start: 42 outliers final: 35 residues processed: 106 average time/residue: 0.0776 time to fit residues: 11.2382 Evaluate side-chains 112 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 75 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 395 LYS Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 876 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 66 optimal weight: 0.0870 chunk 67 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.192760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.156317 restraints weight = 6181.001| |-----------------------------------------------------------------------------| r_work (start): 0.5337 rms_B_bonded: 2.24 r_work: 0.5119 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.5119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6972 Z= 0.147 Angle : 0.580 11.672 9462 Z= 0.299 Chirality : 0.048 0.186 1091 Planarity : 0.005 0.065 1206 Dihedral : 4.935 56.823 945 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.99 % Allowed : 18.11 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.29), residues: 871 helix: 0.56 (0.78), residues: 59 sheet: -0.60 (0.30), residues: 313 loop : -0.47 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 868 TYR 0.015 0.001 TYR A 717 PHE 0.010 0.001 PHE A 556 TRP 0.014 0.002 TRP A 298 HIS 0.003 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 6972) covalent geometry : angle 0.57963 ( 9462) hydrogen bonds : bond 0.03271 ( 199) hydrogen bonds : angle 5.91141 ( 549) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 78 time to evaluate : 0.240 Fit side-chains REVERT: A 108 GLN cc_start: 0.7918 (tp-100) cc_final: 0.6417 (mp10) REVERT: A 118 ARG cc_start: 0.6003 (mmm-85) cc_final: 0.5534 (mmm-85) REVERT: A 128 LYS cc_start: 0.7249 (mmtp) cc_final: 0.6686 (mtmm) REVERT: A 160 LYS cc_start: 0.7570 (tttt) cc_final: 0.7196 (mtmm) REVERT: A 279 TYR cc_start: 0.6590 (OUTLIER) cc_final: 0.5771 (t80) REVERT: A 340 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7611 (mpp) REVERT: A 342 GLU cc_start: 0.6484 (mt-10) cc_final: 0.6170 (mm-30) REVERT: A 386 ASN cc_start: 0.5358 (t0) cc_final: 0.5124 (m-40) REVERT: A 439 MET cc_start: 0.7554 (ttm) cc_final: 0.7191 (ttp) REVERT: A 626 MET cc_start: 0.6256 (mtt) cc_final: 0.6017 (mtp) REVERT: A 705 MET cc_start: 0.6994 (ttp) cc_final: 0.6762 (tmm) REVERT: A 846 GLU cc_start: 0.6905 (tt0) cc_final: 0.6456 (mp0) REVERT: A 859 LYS cc_start: 0.7504 (tptt) cc_final: 0.7213 (mtmt) outliers start: 38 outliers final: 34 residues processed: 103 average time/residue: 0.0692 time to fit residues: 9.7356 Evaluate side-chains 114 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 78 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 395 LYS Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 896 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.185081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.148879 restraints weight = 6380.658| |-----------------------------------------------------------------------------| r_work (start): 0.5280 rms_B_bonded: 2.26 r_work: 0.5054 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.5054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6972 Z= 0.218 Angle : 0.662 10.950 9462 Z= 0.342 Chirality : 0.051 0.189 1091 Planarity : 0.006 0.066 1206 Dihedral : 5.361 54.344 945 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 5.25 % Allowed : 17.72 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.29), residues: 871 helix: 0.42 (0.78), residues: 59 sheet: -0.86 (0.29), residues: 316 loop : -0.68 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 910 TYR 0.022 0.002 TYR A 695 PHE 0.016 0.002 PHE A 87 TRP 0.012 0.002 TRP A 298 HIS 0.003 0.001 HIS A 632 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 6972) covalent geometry : angle 0.66195 ( 9462) hydrogen bonds : bond 0.03676 ( 199) hydrogen bonds : angle 6.30590 ( 549) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 77 time to evaluate : 0.172 Fit side-chains REVERT: A 118 ARG cc_start: 0.6068 (mmm-85) cc_final: 0.5608 (mmm-85) REVERT: A 128 LYS cc_start: 0.7315 (mmtp) cc_final: 0.6789 (mtmm) REVERT: A 160 LYS cc_start: 0.7569 (tttt) cc_final: 0.7170 (mtmm) REVERT: A 279 TYR cc_start: 0.6628 (OUTLIER) cc_final: 0.5781 (t80) REVERT: A 291 GLU cc_start: 0.7207 (tp30) cc_final: 0.6443 (tt0) REVERT: A 340 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.7854 (mpt) REVERT: A 342 GLU cc_start: 0.6538 (mt-10) cc_final: 0.6168 (mm-30) REVERT: A 386 ASN cc_start: 0.5525 (t0) cc_final: 0.5166 (m-40) REVERT: A 626 MET cc_start: 0.6238 (mtt) cc_final: 0.5949 (mtp) REVERT: A 705 MET cc_start: 0.7333 (ttp) cc_final: 0.7092 (tmm) REVERT: A 846 GLU cc_start: 0.7171 (tt0) cc_final: 0.6709 (mp0) REVERT: A 859 LYS cc_start: 0.7498 (tptt) cc_final: 0.7207 (mtmt) outliers start: 40 outliers final: 37 residues processed: 105 average time/residue: 0.0672 time to fit residues: 9.6639 Evaluate side-chains 115 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 76 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 395 LYS Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 854 PHE Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 896 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 37 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 0.3980 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.0980 chunk 81 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 86 optimal weight: 0.0970 chunk 27 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.191916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.156342 restraints weight = 6236.688| |-----------------------------------------------------------------------------| r_work (start): 0.5367 rms_B_bonded: 2.20 r_work: 0.5152 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.5152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6972 Z= 0.112 Angle : 0.547 10.900 9462 Z= 0.285 Chirality : 0.047 0.166 1091 Planarity : 0.005 0.066 1206 Dihedral : 4.975 59.180 945 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.67 % Allowed : 19.16 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.29), residues: 871 helix: -0.06 (0.73), residues: 66 sheet: -0.64 (0.30), residues: 308 loop : -0.57 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 868 TYR 0.017 0.001 TYR A 717 PHE 0.011 0.001 PHE A 126 TRP 0.019 0.002 TRP A 298 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6972) covalent geometry : angle 0.54669 ( 9462) hydrogen bonds : bond 0.03138 ( 199) hydrogen bonds : angle 5.87843 ( 549) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1749.68 seconds wall clock time: 30 minutes 34.93 seconds (1834.93 seconds total)