Starting phenix.real_space_refine on Thu Jul 2 06:03:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y48_72474/07_2026/9y48_72474.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y48_72474/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9y48_72474/07_2026/9y48_72474.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y48_72474/07_2026/9y48_72474.map" model { file = "/net/cci-nas-00/data/ceres_data/9y48_72474/07_2026/9y48_72474.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y48_72474/07_2026/9y48_72474.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Time building chain proxies: 1.26, 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: 0.42 Conformation dependent library (CDL) restraints added in 259.0 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: 0.24 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: 1.07 Time building geometry restraints manager: 0.59 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: 1.910 Set stop_for_unknowns flag: 0.010 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.220 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: 0.010 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6323 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/Z covalent geometry : bond 0.00315 / 0.16 ( 6972) covalent geometry : angle 0.68758 / 0.40 ( 9462) hydrogen bonds : bond 0.15793 / 10.12 ( 199) hydrogen bonds : angle 7.89070 / 5.42 ( 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 : 0.200 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: 0.0635 time to fit residues: 9.4962 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 : 0.172 ------------------------------------------------------------------------------- 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... 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 = 0.4622 r_free = 0.4622 target = 0.206961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.172957 restraints weight = 5895.692| |-----------------------------------------------------------------------------| r_work (start): 0.5516 rms_B_bonded: 2.20 r_work: 0.5272 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.5272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6972 Z= 0.122 Angle : 0.568 6.836 9462 Z= 0.298 Chirality : 0.048 0.221 1091 Planarity : 0.005 0.057 1206 Dihedral : 4.922 55.496 947 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.15 % Allowed : 14.30 % 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: -0.16 (0.29), residues: 871 helix: -0.05 (0.68), residues: 59 sheet: 0.04 (0.29), residues: 322 loop : -0.11 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 868 TYR 0.014 0.001 TYR A 695 PHE 0.014 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/Z covalent geometry : bond 0.00273 / 0.12 ( 6972) covalent geometry : angle 0.56812 / 0.30 ( 9462) hydrogen bonds : bond 0.03757 / 2.42 ( 199) hydrogen bonds : angle 6.25960 / 4.35 ( 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 106 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.158 Fit side-chains REVERT: A 108 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6044 (mp10) REVERT: A 160 LYS cc_start: 0.7535 (tttt) cc_final: 0.7205 (mtmm) REVERT: A 279 TYR cc_start: 0.6493 (OUTLIER) cc_final: 0.5548 (t80) REVERT: A 342 GLU cc_start: 0.6400 (mt-10) cc_final: 0.6113 (mm-30) REVERT: A 347 TYR cc_start: 0.6353 (m-10) cc_final: 0.6048 (m-80) REVERT: A 579 VAL cc_start: 0.6646 (t) cc_final: 0.6403 (m) REVERT: A 672 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7393 (tt0) REVERT: A 859 LYS cc_start: 0.7272 (tptt) cc_final: 0.7059 (mtmt) REVERT: A 929 GLN cc_start: 0.7094 (tm-30) cc_final: 0.6864 (tt0) outliers start: 24 outliers final: 11 residues processed: 97 average time/residue: 0.0666 time to fit residues: 8.8810 Evaluate side-chains 88 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 279 TYR 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: 0.9990 chunk 67 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.0470 chunk 0 optimal weight: 7.9990 chunk 71 optimal weight: 0.3980 chunk 74 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN A 136 ASN 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 = 0.4594 r_free = 0.4594 target = 0.203708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.169491 restraints weight = 5856.022| |-----------------------------------------------------------------------------| r_work (start): 0.5500 rms_B_bonded: 2.29 r_work: 0.5258 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.5258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6972 Z= 0.112 Angle : 0.525 6.324 9462 Z= 0.274 Chirality : 0.047 0.177 1091 Planarity : 0.004 0.055 1206 Dihedral : 4.751 57.005 946 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.76 % Allowed : 15.49 % Favored : 81.76 % 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: -0.08 (0.29), residues: 871 helix: 0.30 (0.72), residues: 59 sheet: 0.12 (0.29), residues: 316 loop : -0.11 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 520 TYR 0.013 0.001 TYR A 717 PHE 0.010 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/Z covalent geometry : bond 0.00256 / 0.11 ( 6972) covalent geometry : angle 0.52497 / 0.27 ( 9462) hydrogen bonds : bond 0.03451 / 2.21 ( 199) hydrogen bonds : angle 5.92500 / 4.14 ( 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 102 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.165 Fit side-chains REVERT: A 128 LYS cc_start: 0.7124 (mmtp) cc_final: 0.6725 (mtmm) REVERT: A 160 LYS cc_start: 0.7550 (tttt) cc_final: 0.7225 (mtmm) REVERT: A 279 TYR cc_start: 0.6524 (OUTLIER) cc_final: 0.5529 (t80) REVERT: A 342 GLU cc_start: 0.6486 (mt-10) cc_final: 0.6167 (mm-30) REVERT: A 347 TYR cc_start: 0.6390 (m-10) cc_final: 0.6061 (m-80) REVERT: A 626 MET cc_start: 0.6121 (mtt) cc_final: 0.5677 (mtp) REVERT: A 672 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7470 (tt0) REVERT: A 859 LYS cc_start: 0.7374 (tptt) cc_final: 0.7104 (mtmt) REVERT: A 929 GLN cc_start: 0.7130 (tm-30) cc_final: 0.6882 (tt0) outliers start: 21 outliers final: 15 residues processed: 95 average time/residue: 0.0646 time to fit residues: 8.5078 Evaluate side-chains 89 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 279 TYR 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 465 THR Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 876 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 15 optimal weight: 0.0470 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.197541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.162082 restraints weight = 6049.162| |-----------------------------------------------------------------------------| r_work (start): 0.5408 rms_B_bonded: 2.16 r_work: 0.5185 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.5185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6972 Z= 0.144 Angle : 0.554 6.158 9462 Z= 0.288 Chirality : 0.048 0.168 1091 Planarity : 0.005 0.068 1206 Dihedral : 4.803 58.848 945 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.67 % Allowed : 15.35 % Favored : 80.97 % 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: -0.28 (0.29), residues: 871 helix: 0.44 (0.75), residues: 59 sheet: -0.12 (0.29), residues: 314 loop : -0.20 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 125 TYR 0.015 0.001 TYR A 695 PHE 0.012 0.002 PHE A 556 TRP 0.017 0.002 TRP A 298 HIS 0.005 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 6972) covalent geometry : angle 0.55445 / 0.29 ( 9462) hydrogen bonds : bond 0.03338 / 2.16 ( 199) hydrogen bonds : angle 5.84393 / 4.08 ( 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 110 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.238 Fit side-chains REVERT: A 128 LYS cc_start: 0.7099 (mmtp) cc_final: 0.6679 (mtmm) REVERT: A 160 LYS cc_start: 0.7556 (tttt) cc_final: 0.7186 (mtmm) REVERT: A 279 TYR cc_start: 0.6493 (OUTLIER) cc_final: 0.5547 (t80) REVERT: A 342 GLU cc_start: 0.6506 (mt-10) cc_final: 0.6245 (mm-30) REVERT: A 626 MET cc_start: 0.6205 (mtt) cc_final: 0.5752 (mtp) REVERT: A 859 LYS cc_start: 0.7413 (tptt) cc_final: 0.7114 (mtmt) REVERT: A 929 GLN cc_start: 0.7094 (tm-30) cc_final: 0.6873 (tt0) outliers start: 28 outliers final: 19 residues processed: 100 average time/residue: 0.0695 time to fit residues: 9.4982 Evaluate side-chains 95 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 229 ILE Chi-restraints excluded: chain A residue 279 TYR 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 659 MET 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 63 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.196567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.162216 restraints weight = 6142.196| |-----------------------------------------------------------------------------| r_work (start): 0.5418 rms_B_bonded: 2.19 r_work: 0.5194 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.5194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6972 Z= 0.132 Angle : 0.544 8.131 9462 Z= 0.282 Chirality : 0.047 0.169 1091 Planarity : 0.005 0.060 1206 Dihedral : 4.786 58.683 945 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.07 % Allowed : 15.49 % Favored : 80.45 % 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: -0.32 (0.29), residues: 871 helix: 0.53 (0.76), residues: 59 sheet: -0.19 (0.30), residues: 308 loop : -0.22 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 520 TYR 0.011 0.001 TYR A 717 PHE 0.010 0.001 PHE A 535 TRP 0.018 0.002 TRP A 298 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 6972) covalent geometry : angle 0.54446 / 0.28 ( 9462) hydrogen bonds : bond 0.03211 / 2.07 ( 199) hydrogen bonds : angle 5.78021 / 4.06 ( 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 108 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 128 LYS cc_start: 0.7206 (mmtp) cc_final: 0.6776 (mtmm) REVERT: A 160 LYS cc_start: 0.7572 (tttt) cc_final: 0.7316 (mtmm) REVERT: A 279 TYR cc_start: 0.6415 (OUTLIER) cc_final: 0.5570 (t80) REVERT: A 342 GLU cc_start: 0.6470 (mt-10) cc_final: 0.6261 (mm-30) REVERT: A 626 MET cc_start: 0.6254 (mtt) cc_final: 0.5869 (mtp) REVERT: A 859 LYS cc_start: 0.7433 (tptt) cc_final: 0.7203 (mtmt) outliers start: 31 outliers final: 28 residues processed: 99 average time/residue: 0.0706 time to fit residues: 9.4972 Evaluate side-chains 99 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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 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 277 SER Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 286 ILE 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 475 LYS 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 18 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 85 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.192512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.157773 restraints weight = 6228.097| |-----------------------------------------------------------------------------| r_work (start): 0.5373 rms_B_bonded: 2.43 r_work: 0.5137 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.5137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6972 Z= 0.160 Angle : 0.581 8.000 9462 Z= 0.303 Chirality : 0.048 0.165 1091 Planarity : 0.005 0.058 1206 Dihedral : 4.945 59.924 945 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.12 % Allowed : 15.62 % 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: -0.51 (0.29), residues: 871 helix: 1.18 (0.81), residues: 53 sheet: -0.45 (0.30), residues: 315 loop : -0.34 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 868 TYR 0.011 0.001 TYR A 388 PHE 0.013 0.002 PHE A 556 TRP 0.017 0.002 TRP A 298 HIS 0.003 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 6972) covalent geometry : angle 0.58077 / 0.30 ( 9462) hydrogen bonds : bond 0.03391 / 2.16 ( 199) hydrogen bonds : angle 5.85755 / 4.11 ( 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 114 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 75 time to evaluate : 0.148 Fit side-chains REVERT: A 128 LYS cc_start: 0.7266 (mmtp) cc_final: 0.6880 (mtmm) REVERT: A 160 LYS cc_start: 0.7596 (tttt) cc_final: 0.7307 (mtmm) REVERT: A 279 TYR cc_start: 0.6480 (OUTLIER) cc_final: 0.5636 (t80) REVERT: A 342 GLU cc_start: 0.6497 (mt-10) cc_final: 0.6266 (mm-30) REVERT: A 350 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6526 (mp) REVERT: A 386 ASN cc_start: 0.5521 (t0) cc_final: 0.5227 (m-40) REVERT: A 626 MET cc_start: 0.6260 (mtt) cc_final: 0.5922 (mtp) REVERT: A 859 LYS cc_start: 0.7470 (tptt) cc_final: 0.7257 (mtmt) outliers start: 39 outliers final: 30 residues processed: 101 average time/residue: 0.0570 time to fit residues: 7.9943 Evaluate side-chains 103 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 71 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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 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 277 SER Chi-restraints excluded: chain A residue 279 TYR 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 401 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 445 ILE 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 25 optimal weight: 0.0020 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.196482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.160197 restraints weight = 6055.611| |-----------------------------------------------------------------------------| r_work (start): 0.5384 rms_B_bonded: 2.23 r_work: 0.5159 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.5159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6972 Z= 0.120 Angle : 0.532 7.819 9462 Z= 0.279 Chirality : 0.047 0.163 1091 Planarity : 0.005 0.057 1206 Dihedral : 4.749 56.995 945 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.54 % Allowed : 16.67 % 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: -0.41 (0.29), residues: 871 helix: 1.35 (0.83), residues: 53 sheet: -0.44 (0.30), residues: 320 loop : -0.23 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 868 TYR 0.016 0.001 TYR A 717 PHE 0.012 0.001 PHE A 126 TRP 0.017 0.002 TRP A 298 HIS 0.004 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 6972) covalent geometry : angle 0.53206 / 0.28 ( 9462) hydrogen bonds : bond 0.03158 / 2.01 ( 199) hydrogen bonds : angle 5.68592 / 4.00 ( 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 102 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: A 128 LYS cc_start: 0.7143 (mmtp) cc_final: 0.6598 (mtmm) REVERT: A 160 LYS cc_start: 0.7613 (tttt) cc_final: 0.7192 (mtmm) REVERT: A 279 TYR cc_start: 0.6463 (OUTLIER) cc_final: 0.5568 (t80) REVERT: A 342 GLU cc_start: 0.6606 (mt-10) cc_final: 0.6272 (mm-30) REVERT: A 386 ASN cc_start: 0.5384 (t0) cc_final: 0.5075 (m-40) REVERT: A 626 MET cc_start: 0.6163 (mtt) cc_final: 0.5790 (mtp) REVERT: A 859 LYS cc_start: 0.7380 (tptt) cc_final: 0.7057 (mtmt) outliers start: 27 outliers final: 26 residues processed: 93 average time/residue: 0.0624 time to fit residues: 8.0307 Evaluate side-chains 99 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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 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 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 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 0.0870 chunk 69 optimal weight: 0.2980 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.196866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.161029 restraints weight = 6169.500| |-----------------------------------------------------------------------------| r_work (start): 0.5390 rms_B_bonded: 2.19 r_work: 0.5165 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.5165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6972 Z= 0.113 Angle : 0.521 7.565 9462 Z= 0.274 Chirality : 0.047 0.156 1091 Planarity : 0.005 0.056 1206 Dihedral : 4.681 57.401 945 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.20 % Allowed : 16.27 % Favored : 79.53 % 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: -0.33 (0.30), residues: 871 helix: 1.31 (0.82), residues: 53 sheet: -0.35 (0.30), residues: 316 loop : -0.19 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 868 TYR 0.013 0.001 TYR A 717 PHE 0.011 0.001 PHE A 126 TRP 0.015 0.002 TRP A 298 HIS 0.004 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 6972) covalent geometry : angle 0.52119 / 0.27 ( 9462) hydrogen bonds : bond 0.03138 / 1.98 ( 199) hydrogen bonds : angle 5.63921 / 3.97 ( 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 106 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 74 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 128 LYS cc_start: 0.7147 (mmtp) cc_final: 0.6662 (mtmm) REVERT: A 160 LYS cc_start: 0.7631 (tttt) cc_final: 0.7245 (mtmm) REVERT: A 279 TYR cc_start: 0.6498 (OUTLIER) cc_final: 0.5651 (t80) REVERT: A 342 GLU cc_start: 0.6598 (mt-10) cc_final: 0.6306 (mm-30) REVERT: A 350 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.6668 (mp) REVERT: A 386 ASN cc_start: 0.5408 (t0) cc_final: 0.5106 (m-40) REVERT: A 626 MET cc_start: 0.6188 (mtt) cc_final: 0.5855 (mtp) REVERT: A 859 LYS cc_start: 0.7427 (tptt) cc_final: 0.7182 (mtmt) outliers start: 32 outliers final: 26 residues processed: 97 average time/residue: 0.0575 time to fit residues: 7.7859 Evaluate side-chains 103 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 279 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 334 ILE 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 445 ILE 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 66 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 86 optimal weight: 0.0470 chunk 63 optimal weight: 0.8980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.196147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.159967 restraints weight = 6105.839| |-----------------------------------------------------------------------------| r_work (start): 0.5365 rms_B_bonded: 2.22 r_work: 0.5142 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.5142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6972 Z= 0.133 Angle : 0.546 7.638 9462 Z= 0.285 Chirality : 0.047 0.175 1091 Planarity : 0.005 0.076 1206 Dihedral : 4.794 58.607 945 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.46 % Allowed : 16.14 % Favored : 79.40 % 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: -0.39 (0.30), residues: 871 helix: 1.31 (0.83), residues: 53 sheet: -0.43 (0.30), residues: 316 loop : -0.21 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 868 TYR 0.019 0.001 TYR A 695 PHE 0.011 0.001 PHE A 556 TRP 0.016 0.002 TRP A 298 HIS 0.003 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 6972) covalent geometry : angle 0.54589 / 0.29 ( 9462) hydrogen bonds : bond 0.03202 / 2.05 ( 199) hydrogen bonds : angle 5.73074 / 4.03 ( 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 106 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 72 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 128 LYS cc_start: 0.7121 (mmtp) cc_final: 0.6656 (mtmm) REVERT: A 160 LYS cc_start: 0.7585 (tttt) cc_final: 0.7204 (mtmm) REVERT: A 279 TYR cc_start: 0.6588 (OUTLIER) cc_final: 0.5695 (t80) REVERT: A 342 GLU cc_start: 0.6578 (mt-10) cc_final: 0.6142 (mm-30) REVERT: A 350 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6638 (mp) REVERT: A 386 ASN cc_start: 0.5428 (t0) cc_final: 0.5103 (m-40) REVERT: A 626 MET cc_start: 0.6198 (mtt) cc_final: 0.5839 (mtp) REVERT: A 686 THR cc_start: 0.6095 (OUTLIER) cc_final: 0.5766 (p) REVERT: A 734 ILE cc_start: 0.7477 (tp) cc_final: 0.7189 (tp) REVERT: A 859 LYS cc_start: 0.7477 (tptt) cc_final: 0.7181 (mtmt) outliers start: 34 outliers final: 30 residues processed: 97 average time/residue: 0.0644 time to fit residues: 8.7369 Evaluate side-chains 105 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 72 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 573 VAL Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 686 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.0370 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 74 optimal weight: 7.9990 chunk 67 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.196117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.159882 restraints weight = 6116.730| |-----------------------------------------------------------------------------| r_work (start): 0.5376 rms_B_bonded: 2.24 r_work: 0.5160 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.5160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.3533 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= 0.114 Angle : 0.519 7.618 9462 Z= 0.272 Chirality : 0.047 0.158 1091 Planarity : 0.005 0.076 1206 Dihedral : 4.697 57.698 945 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.46 % Allowed : 16.27 % 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: -0.30 (0.30), residues: 871 helix: 1.23 (0.82), residues: 54 sheet: -0.37 (0.30), residues: 316 loop : -0.14 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 868 TYR 0.019 0.001 TYR A 717 PHE 0.010 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/Z covalent geometry : bond 0.00264 / 0.11 ( 6972) covalent geometry : angle 0.51944 / 0.27 ( 9462) hydrogen bonds : bond 0.03070 / 1.97 ( 199) hydrogen bonds : angle 5.61298 / 3.95 ( 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 109 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 0.174 Fit side-chains REVERT: A 128 LYS cc_start: 0.7089 (mmtp) cc_final: 0.6593 (mtmm) REVERT: A 160 LYS cc_start: 0.7590 (tttt) cc_final: 0.7209 (mtmm) REVERT: A 279 TYR cc_start: 0.6556 (OUTLIER) cc_final: 0.5701 (t80) REVERT: A 342 GLU cc_start: 0.6582 (mt-10) cc_final: 0.6109 (mm-30) REVERT: A 386 ASN cc_start: 0.5411 (t0) cc_final: 0.5112 (m-40) REVERT: A 626 MET cc_start: 0.6231 (mtt) cc_final: 0.5880 (mtp) REVERT: A 664 ARG cc_start: 0.7065 (mtm180) cc_final: 0.6863 (mtm180) REVERT: A 686 THR cc_start: 0.6064 (OUTLIER) cc_final: 0.5727 (p) REVERT: A 734 ILE cc_start: 0.7313 (tp) cc_final: 0.7040 (tp) REVERT: A 846 GLU cc_start: 0.6907 (tt0) cc_final: 0.6213 (mp0) REVERT: A 859 LYS cc_start: 0.7600 (tptt) cc_final: 0.7311 (mtmt) outliers start: 34 outliers final: 31 residues processed: 100 average time/residue: 0.0699 time to fit residues: 9.7616 Evaluate side-chains 106 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 399 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 445 ILE 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 573 VAL Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 686 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 37 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 0.0020 chunk 7 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 56 optimal weight: 0.3980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.195689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.160132 restraints weight = 6126.987| |-----------------------------------------------------------------------------| r_work (start): 0.5391 rms_B_bonded: 2.19 r_work: 0.5165 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.5165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6972 Z= 0.110 Angle : 0.516 7.537 9462 Z= 0.269 Chirality : 0.047 0.161 1091 Planarity : 0.005 0.075 1206 Dihedral : 4.688 58.296 945 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.20 % Allowed : 16.80 % Favored : 79.00 % 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: -0.26 (0.30), residues: 871 helix: 1.38 (0.83), residues: 53 sheet: -0.35 (0.30), residues: 316 loop : -0.11 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 868 TYR 0.016 0.001 TYR A 717 PHE 0.010 0.001 PHE A 126 TRP 0.015 0.002 TRP A 298 HIS 0.003 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 6972) covalent geometry : angle 0.51591 / 0.27 ( 9462) hydrogen bonds : bond 0.03010 / 1.95 ( 199) hydrogen bonds : angle 5.59186 / 3.93 ( 549) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1623.18 seconds wall clock time: 28 minutes 28.41 seconds (1708.41 seconds total)