Starting phenix.real_space_refine on Fri Sep 11 00:31:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w89_65740/09_2026/9w89_65740.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w89_65740/09_2026/9w89_65740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w89_65740/09_2026/9w89_65740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w89_65740/09_2026/9w89_65740.map" model { file = "/net/cci-nas-00/data/ceres_data/9w89_65740/09_2026/9w89_65740.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w89_65740/09_2026/9w89_65740.cif" } resolution = 2.89 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= 0.101 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: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 3675 2.51 5 N 1023 2.21 5 O 1125 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5862 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4914 Classifications: {'peptide': 631} Link IDs: {'PCIS': 2, 'PTRANS': 46, 'TRANS': 582} Chain breaks: 1 Chain: "B" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 948 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 120} Time building chain proxies: 1.40, per 1000 atoms: 0.24 Number of scatterers: 5862 At special positions: 0 Unit cell: (62.216, 94.536, 144.632, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1125 8.00 N 1023 7.00 C 3675 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 190 " distance=2.03 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 93 " distance=2.03 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 268 " - pdb=" SG CYS A 285 " distance=2.03 Simple disulfide: pdb=" SG CYS A 475 " - pdb=" SG CYS A 540 " distance=2.03 Simple disulfide: pdb=" SG CYS A 488 " - pdb=" SG CYS A 520 " distance=2.03 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 494 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 685 " - pdb=" SG CYS A 697 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 33 " - pdb=" SG CYS B 100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 169.3 milliseconds 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1394 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 22 sheets defined 6.6% alpha, 46.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 69 through 75 removed outlier: 4.086A pdb=" N VAL A 73 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 664 through 673 Processing helix chain 'A' and resid 676 through 681 Processing helix chain 'A' and resid 682 through 685 Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.660A pdb=" N THR B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 105 removed outlier: 3.623A pdb=" N GLN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 84 Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 103 removed outlier: 6.648A pdb=" N GLN A 114 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE A 102 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS A 112 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 10.074A pdb=" N SER A 116 " --> pdb=" O MET A 135 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N MET A 135 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LYS A 131 " --> pdb=" O GLY A 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 103 removed outlier: 6.648A pdb=" N GLN A 114 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE A 102 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS A 112 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N HIS A 164 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 9.178A pdb=" N LEU A 117 " --> pdb=" O MET A 162 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N MET A 162 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 9.483A pdb=" N ILE A 119 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 10.929A pdb=" N GLY A 160 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 15.943A pdb=" N ILE A 121 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 18.949A pdb=" N ILE A 158 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 149 through 151 removed outlier: 4.932A pdb=" N PHE A 194 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N THR A 177 " --> pdb=" O HIS A 192 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N HIS A 192 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLY A 179 " --> pdb=" O CYS A 190 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N CYS A 190 " --> pdb=" O GLY A 179 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N THR A 181 " --> pdb=" O HIS A 188 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N HIS A 188 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 214 through 221 Processing sheet with id=AA6, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA7, first strand: chain 'A' and resid 240 through 241 Processing sheet with id=AA8, first strand: chain 'A' and resid 246 through 249 Processing sheet with id=AA9, first strand: chain 'A' and resid 340 through 343 removed outlier: 3.551A pdb=" N VAL A 382 " --> pdb=" O MET A 350 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 372 through 376 Processing sheet with id=AB2, first strand: chain 'A' and resid 426 through 434 removed outlier: 4.110A pdb=" N ASP A 707 " --> pdb=" O LYS A 586 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS A 586 " --> pdb=" O ASP A 707 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 441 through 445 removed outlier: 7.878A pdb=" N MET A 457 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N LEU A 562 " --> pdb=" O MET A 457 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU A 459 " --> pdb=" O ARG A 560 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ARG A 560 " --> pdb=" O LEU A 459 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 461 " --> pdb=" O LYS A 558 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 441 through 445 Processing sheet with id=AB5, first strand: chain 'A' and resid 468 through 474 removed outlier: 5.869A pdb=" N LEU A 470 " --> pdb=" O ARG A 549 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG A 549 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR A 472 " --> pdb=" O ALA A 547 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 477 through 480 Processing sheet with id=AB7, first strand: chain 'A' and resid 477 through 480 Processing sheet with id=AB8, first strand: chain 'A' and resid 513 through 514 Processing sheet with id=AB9, first strand: chain 'A' and resid 629 through 631 Processing sheet with id=AC1, first strand: chain 'A' and resid 646 through 647 Processing sheet with id=AC2, first strand: chain 'B' and resid 2 through 7 Processing sheet with id=AC3, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.916A pdb=" N VAL B 12 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N CYS B 33 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY B 50 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.916A pdb=" N VAL B 12 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N CYS B 95 " --> pdb=" O TRP B 113 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N TRP B 113 " --> pdb=" O CYS B 95 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLU B 97 " --> pdb=" O PHE B 111 " (cutoff:3.500A) 218 hydrogen bonds defined for protein. 507 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: 1.05 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1937 1.34 - 1.46: 1401 1.46 - 1.58: 2626 1.58 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 6016 Sorted by residual: bond pdb=" N ASP A 584 " pdb=" CA ASP A 584 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.73e-01 bond pdb=" CA PRO A 323 " pdb=" C PRO A 323 " ideal model delta sigma weight residual 1.526 1.516 0.010 1.13e-02 7.83e+03 7.47e-01 bond pdb=" C ILE A 702 " pdb=" O ILE A 702 " ideal model delta sigma weight residual 1.232 1.240 -0.009 1.01e-02 9.80e+03 7.09e-01 bond pdb=" CA GLU A 89 " pdb=" CB GLU A 89 " ideal model delta sigma weight residual 1.532 1.544 -0.012 1.51e-02 4.39e+03 5.92e-01 bond pdb=" C THR A 152 " pdb=" O THR A 152 " ideal model delta sigma weight residual 1.234 1.243 -0.009 1.17e-02 7.31e+03 5.66e-01 ... (remaining 6011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 7821 1.11 - 2.21: 279 2.21 - 3.32: 67 3.32 - 4.42: 20 4.42 - 5.53: 3 Bond angle restraints: 8190 Sorted by residual: angle pdb=" C GLY A 88 " pdb=" N GLU A 89 " pdb=" CA GLU A 89 " ideal model delta sigma weight residual 122.61 127.48 -4.87 1.56e+00 4.11e-01 9.74e+00 angle pdb=" N GLY A 517 " pdb=" CA GLY A 517 " pdb=" C GLY A 517 " ideal model delta sigma weight residual 110.56 114.62 -4.06 1.36e+00 5.41e-01 8.93e+00 angle pdb=" N THR A 152 " pdb=" CA THR A 152 " pdb=" C THR A 152 " ideal model delta sigma weight residual 111.96 107.78 4.18 1.41e+00 5.03e-01 8.78e+00 angle pdb=" CA GLY A 88 " pdb=" C GLY A 88 " pdb=" O GLY A 88 " ideal model delta sigma weight residual 121.77 119.88 1.89 8.60e-01 1.35e+00 4.83e+00 angle pdb=" N SER A 153 " pdb=" CA SER A 153 " pdb=" C SER A 153 " ideal model delta sigma weight residual 114.39 111.46 2.93 1.45e+00 4.76e-01 4.09e+00 ... (remaining 8185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.41: 3279 15.41 - 30.81: 273 30.81 - 46.22: 60 46.22 - 61.63: 8 61.63 - 77.03: 6 Dihedral angle restraints: 3626 sinusoidal: 1442 harmonic: 2184 Sorted by residual: dihedral pdb=" CB CYS A 268 " pdb=" SG CYS A 268 " pdb=" SG CYS A 285 " pdb=" CB CYS A 285 " ideal model delta sinusoidal sigma weight residual 93.00 164.90 -71.90 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS A 685 " pdb=" SG CYS A 685 " pdb=" SG CYS A 697 " pdb=" CB CYS A 697 " ideal model delta sinusoidal sigma weight residual 93.00 137.90 -44.90 1 1.00e+01 1.00e-02 2.80e+01 dihedral pdb=" CA GLN B 71 " pdb=" C GLN B 71 " pdb=" N ASP B 72 " pdb=" CA ASP B 72 " ideal model delta harmonic sigma weight residual 180.00 157.81 22.19 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 3623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 541 0.028 - 0.057: 218 0.057 - 0.085: 50 0.085 - 0.113: 65 0.113 - 0.142: 15 Chirality restraints: 889 Sorted by residual: chirality pdb=" CA GLU A 89 " pdb=" N GLU A 89 " pdb=" C GLU A 89 " pdb=" CB GLU A 89 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA ILE A 166 " pdb=" N ILE A 166 " pdb=" C ILE A 166 " pdb=" CB ILE A 166 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA PRO B 87 " pdb=" N PRO B 87 " pdb=" C PRO B 87 " pdb=" CB PRO B 87 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.84e-01 ... (remaining 886 not shown) Planarity restraints: 1072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 86 " -0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO B 87 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 87 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 87 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 192 " -0.016 5.00e-02 4.00e+02 2.35e-02 8.81e-01 pdb=" N PRO A 193 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 193 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 193 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 633 " -0.015 5.00e-02 4.00e+02 2.23e-02 7.95e-01 pdb=" N PRO A 634 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 634 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 634 " -0.013 5.00e-02 4.00e+02 ... (remaining 1069 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 871 2.77 - 3.30: 5216 3.30 - 3.83: 9750 3.83 - 4.37: 11727 4.37 - 4.90: 20368 Nonbonded interactions: 47932 Sorted by model distance: nonbonded pdb=" OG1 THR A 240 " pdb=" OD1 ASN A 296 " model vdw 2.232 3.040 nonbonded pdb=" OG1 THR A 633 " pdb=" OG SER A 636 " model vdw 2.235 3.040 nonbonded pdb=" OH TYR A 477 " pdb=" O ALA A 662 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR A 436 " pdb=" OH TYR A 441 " model vdw 2.252 3.040 nonbonded pdb=" NH1 ARG A 151 " pdb=" OD2 ASP B 54 " model vdw 2.334 3.120 ... (remaining 47927 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.230 Find NCS groups from input model: 0.030 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:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 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 0.035 6029 Z= 0.148 Angle : 0.543 5.526 8216 Z= 0.298 Chirality : 0.042 0.142 889 Planarity : 0.003 0.029 1072 Dihedral : 11.999 77.032 2193 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.30), residues: 748 helix: -1.71 (0.94), residues: 28 sheet: 0.62 (0.32), residues: 267 loop : 0.19 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 145 TYR 0.011 0.001 TYR A 563 PHE 0.009 0.001 PHE A 165 TRP 0.004 0.001 TRP A 515 HIS 0.005 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 ( 6016) covalent geometry : angle 0.54264 / 0.30 ( 8190) SS BOND : bond 0.00217 / 0.12 ( 13) SS BOND : angle 0.52963 / 0.39 ( 26) hydrogen bonds : bond 0.21692 / 14.09 ( 203) hydrogen bonds : angle 9.44486 / 6.90 ( 507) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 145 ARG cc_start: 0.6512 (ptm-80) cc_final: 0.5613 (ttp80) REVERT: A 172 LYS cc_start: 0.7727 (ptpp) cc_final: 0.7116 (mttm) REVERT: A 184 ARG cc_start: 0.7006 (ptp-110) cc_final: 0.6659 (ptp-170) REVERT: A 185 LYS cc_start: 0.7458 (mtmm) cc_final: 0.6423 (mmtt) REVERT: A 231 GLU cc_start: 0.6956 (pt0) cc_final: 0.6346 (mt-10) REVERT: A 289 GLN cc_start: 0.7003 (mt0) cc_final: 0.6730 (mt0) REVERT: A 313 LEU cc_start: 0.7275 (mt) cc_final: 0.7016 (mm) REVERT: A 332 ARG cc_start: 0.6460 (ttt90) cc_final: 0.6070 (ttp-170) REVERT: A 368 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6557 (mp0) REVERT: A 372 HIS cc_start: 0.6187 (t-90) cc_final: 0.5033 (m170) REVERT: A 379 LYS cc_start: 0.7242 (tttt) cc_final: 0.6937 (tmtt) REVERT: A 487 LYS cc_start: 0.7173 (tttt) cc_final: 0.6799 (tttp) REVERT: A 493 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7129 (mp0) REVERT: A 503 SER cc_start: 0.6798 (t) cc_final: 0.6283 (p) REVERT: A 541 LYS cc_start: 0.7481 (mttt) cc_final: 0.6449 (mmtt) REVERT: A 601 ASN cc_start: 0.7135 (m-40) cc_final: 0.6702 (m-40) REVERT: A 671 LYS cc_start: 0.7108 (ttpp) cc_final: 0.6043 (mppt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.6344 time to fit residues: 75.9672 Evaluate side-chains 95 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 HIS A 196 HIS A 223 GLN A 235 HIS A 258 ASN A 296 ASN A 346 ASN A 398 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.164536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.124881 restraints weight = 5875.599| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.69 r_work: 0.3063 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6029 Z= 0.221 Angle : 0.640 7.396 8216 Z= 0.334 Chirality : 0.049 0.198 889 Planarity : 0.005 0.079 1072 Dihedral : 4.844 23.109 824 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.80 % Allowed : 6.21 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.29), residues: 748 helix: -2.29 (0.83), residues: 28 sheet: 0.38 (0.30), residues: 277 loop : -0.19 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 549 TYR 0.017 0.002 TYR A 548 PHE 0.017 0.002 PHE A 206 TRP 0.011 0.002 TRP A 515 HIS 0.011 0.002 HIS A 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.22 ( 6016) covalent geometry : angle 0.63755 / 0.33 ( 8190) SS BOND : bond 0.00446 / 0.23 ( 13) SS BOND : angle 1.11788 / 0.76 ( 26) hydrogen bonds : bond 0.04018 / 2.70 ( 203) hydrogen bonds : angle 6.75907 / 5.03 ( 507) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 THR cc_start: 0.7677 (p) cc_final: 0.7433 (t) REVERT: A 172 LYS cc_start: 0.8504 (ptpp) cc_final: 0.8204 (mttm) REVERT: A 185 LYS cc_start: 0.8071 (mtmm) cc_final: 0.7526 (mmtt) REVERT: A 231 GLU cc_start: 0.8221 (pt0) cc_final: 0.7818 (mt-10) REVERT: A 254 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7451 (ttmt) REVERT: A 313 LEU cc_start: 0.8643 (mt) cc_final: 0.8432 (mm) REVERT: A 367 GLN cc_start: 0.8078 (tp40) cc_final: 0.7846 (tm-30) REVERT: A 372 HIS cc_start: 0.8057 (t-90) cc_final: 0.7556 (m170) REVERT: A 392 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7817 (tt0) REVERT: A 453 MET cc_start: 0.5281 (OUTLIER) cc_final: 0.3918 (mpt) REVERT: A 457 MET cc_start: 0.6842 (mpt) cc_final: 0.6493 (mpt) REVERT: A 541 LYS cc_start: 0.8647 (mttt) cc_final: 0.8001 (mmtm) REVERT: A 671 LYS cc_start: 0.8260 (ttpp) cc_final: 0.7528 (mppt) REVERT: B 46 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7966 (pt0) outliers start: 18 outliers final: 9 residues processed: 98 average time/residue: 0.6002 time to fit residues: 61.5769 Evaluate side-chains 98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 67 optimal weight: 0.2980 chunk 23 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN A 533 HIS A 678 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.184182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.142426 restraints weight = 5712.521| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.73 r_work: 0.3338 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6029 Z= 0.120 Angle : 0.522 4.815 8216 Z= 0.275 Chirality : 0.045 0.156 889 Planarity : 0.004 0.041 1072 Dihedral : 4.543 21.276 824 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.17 % Allowed : 10.09 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.29), residues: 748 helix: -2.26 (0.83), residues: 28 sheet: 0.44 (0.31), residues: 280 loop : -0.19 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 549 TYR 0.015 0.001 TYR A 548 PHE 0.012 0.001 PHE A 165 TRP 0.006 0.001 TRP A 515 HIS 0.004 0.001 HIS A 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 6016) covalent geometry : angle 0.52088 / 0.27 ( 8190) SS BOND : bond 0.00320 / 0.18 ( 13) SS BOND : angle 0.69126 / 0.48 ( 26) hydrogen bonds : bond 0.03354 / 2.24 ( 203) hydrogen bonds : angle 6.20473 / 4.63 ( 507) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 THR cc_start: 0.7586 (p) cc_final: 0.7318 (t) REVERT: A 162 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8659 (ttt) REVERT: A 172 LYS cc_start: 0.8528 (ptpp) cc_final: 0.8211 (mttm) REVERT: A 185 LYS cc_start: 0.8167 (mtmm) cc_final: 0.7451 (mmtt) REVERT: A 231 GLU cc_start: 0.8258 (pt0) cc_final: 0.7760 (mt-10) REVERT: A 313 LEU cc_start: 0.8615 (mt) cc_final: 0.8331 (mm) REVERT: A 367 GLN cc_start: 0.8135 (tp40) cc_final: 0.7819 (tm-30) REVERT: A 372 HIS cc_start: 0.8123 (t-90) cc_final: 0.7488 (m170) REVERT: A 374 GLU cc_start: 0.8738 (pt0) cc_final: 0.8444 (pp20) REVERT: A 453 MET cc_start: 0.5338 (OUTLIER) cc_final: 0.4028 (mpt) REVERT: A 457 MET cc_start: 0.6725 (OUTLIER) cc_final: 0.6400 (mpt) REVERT: A 541 LYS cc_start: 0.8606 (mttt) cc_final: 0.7905 (mmtm) REVERT: A 671 LYS cc_start: 0.8312 (ttpp) cc_final: 0.7557 (mppt) REVERT: B 46 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7894 (pt0) outliers start: 14 outliers final: 4 residues processed: 102 average time/residue: 0.5699 time to fit residues: 60.8270 Evaluate side-chains 97 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 52 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 36 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 GLN A 258 ASN A 289 GLN A 701 ASN B 71 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.182086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.140313 restraints weight = 5776.941| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.71 r_work: 0.3317 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6029 Z= 0.152 Angle : 0.543 5.964 8216 Z= 0.285 Chirality : 0.046 0.158 889 Planarity : 0.005 0.054 1072 Dihedral : 4.595 21.686 824 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.11 % Allowed : 11.02 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.29), residues: 748 helix: -2.45 (0.79), residues: 28 sheet: 0.35 (0.31), residues: 281 loop : -0.22 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 549 TYR 0.018 0.001 TYR A 548 PHE 0.013 0.002 PHE A 206 TRP 0.007 0.001 TRP A 515 HIS 0.005 0.001 HIS A 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 ( 6016) covalent geometry : angle 0.54194 / 0.28 ( 8190) SS BOND : bond 0.00342 / 0.19 ( 13) SS BOND : angle 0.74968 / 0.56 ( 26) hydrogen bonds : bond 0.03230 / 2.17 ( 203) hydrogen bonds : angle 5.99991 / 4.46 ( 507) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 THR cc_start: 0.7765 (p) cc_final: 0.7485 (t) REVERT: A 172 LYS cc_start: 0.8543 (ptpp) cc_final: 0.8228 (mttm) REVERT: A 185 LYS cc_start: 0.8155 (mtmm) cc_final: 0.7441 (mmtt) REVERT: A 313 LEU cc_start: 0.8644 (mt) cc_final: 0.8368 (mm) REVERT: A 367 GLN cc_start: 0.8180 (tp40) cc_final: 0.7874 (tm-30) REVERT: A 372 HIS cc_start: 0.8215 (t-90) cc_final: 0.7514 (m170) REVERT: A 374 GLU cc_start: 0.8749 (pt0) cc_final: 0.8547 (pp20) REVERT: A 392 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8162 (tt0) REVERT: A 457 MET cc_start: 0.6691 (OUTLIER) cc_final: 0.6444 (mpt) REVERT: A 541 LYS cc_start: 0.8591 (mttt) cc_final: 0.7858 (mmtm) REVERT: A 671 LYS cc_start: 0.8306 (ttpp) cc_final: 0.7577 (mppt) REVERT: B 46 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7929 (pt0) outliers start: 20 outliers final: 9 residues processed: 98 average time/residue: 0.5565 time to fit residues: 57.1437 Evaluate side-chains 99 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 30 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 48 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN A 289 GLN A 701 ASN B 71 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.182335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.140232 restraints weight = 5890.915| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.71 r_work: 0.3307 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6029 Z= 0.148 Angle : 0.532 5.547 8216 Z= 0.280 Chirality : 0.045 0.159 889 Planarity : 0.004 0.047 1072 Dihedral : 4.574 22.099 824 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.11 % Allowed : 12.11 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.29), residues: 748 helix: -2.46 (0.79), residues: 28 sheet: 0.37 (0.31), residues: 281 loop : -0.26 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 549 TYR 0.019 0.001 TYR A 548 PHE 0.011 0.001 PHE A 206 TRP 0.007 0.001 TRP A 515 HIS 0.003 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 6016) covalent geometry : angle 0.53133 / 0.28 ( 8190) SS BOND : bond 0.00320 / 0.17 ( 13) SS BOND : angle 0.70620 / 0.51 ( 26) hydrogen bonds : bond 0.03039 / 2.04 ( 203) hydrogen bonds : angle 5.87728 / 4.36 ( 507) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 THR cc_start: 0.7740 (p) cc_final: 0.7487 (t) REVERT: A 172 LYS cc_start: 0.8408 (ptpp) cc_final: 0.8159 (mttm) REVERT: A 185 LYS cc_start: 0.8058 (mtmm) cc_final: 0.7456 (mmtt) REVERT: A 254 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7054 (tmmm) REVERT: A 372 HIS cc_start: 0.7968 (t-90) cc_final: 0.7416 (m170) REVERT: A 392 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7981 (tt0) REVERT: A 453 MET cc_start: 0.5396 (OUTLIER) cc_final: 0.4139 (mpt) REVERT: A 457 MET cc_start: 0.6748 (OUTLIER) cc_final: 0.6491 (mpt) REVERT: A 541 LYS cc_start: 0.8565 (mttt) cc_final: 0.7870 (mmtm) REVERT: A 671 LYS cc_start: 0.8186 (ttpp) cc_final: 0.7559 (mppt) REVERT: B 46 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7771 (pt0) outliers start: 20 outliers final: 10 residues processed: 99 average time/residue: 0.6042 time to fit residues: 62.4846 Evaluate side-chains 98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 50 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN A 289 GLN B 71 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.182003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.140258 restraints weight = 5779.658| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.71 r_work: 0.3293 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6029 Z= 0.145 Angle : 0.531 5.592 8216 Z= 0.280 Chirality : 0.045 0.157 889 Planarity : 0.004 0.044 1072 Dihedral : 4.556 21.443 824 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.42 % Allowed : 12.73 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.29), residues: 748 helix: -2.46 (0.79), residues: 28 sheet: 0.31 (0.31), residues: 281 loop : -0.26 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 549 TYR 0.020 0.001 TYR A 548 PHE 0.011 0.001 PHE A 206 TRP 0.007 0.001 TRP A 515 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 ( 6016) covalent geometry : angle 0.53001 / 0.28 ( 8190) SS BOND : bond 0.00304 / 0.17 ( 13) SS BOND : angle 0.78508 / 0.52 ( 26) hydrogen bonds : bond 0.02972 / 1.99 ( 203) hydrogen bonds : angle 5.78847 / 4.29 ( 507) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 THR cc_start: 0.7714 (p) cc_final: 0.7467 (t) REVERT: A 162 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8613 (ttt) REVERT: A 172 LYS cc_start: 0.8405 (ptpp) cc_final: 0.8178 (mttm) REVERT: A 185 LYS cc_start: 0.8061 (mtmm) cc_final: 0.7443 (mmtt) REVERT: A 254 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7145 (tmmm) REVERT: A 372 HIS cc_start: 0.7965 (t-90) cc_final: 0.7440 (m170) REVERT: A 392 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7998 (tt0) REVERT: A 453 MET cc_start: 0.5408 (OUTLIER) cc_final: 0.4149 (mpt) REVERT: A 457 MET cc_start: 0.6671 (OUTLIER) cc_final: 0.6428 (mpt) REVERT: A 541 LYS cc_start: 0.8581 (mttt) cc_final: 0.7884 (mmtm) REVERT: A 671 LYS cc_start: 0.8204 (ttpp) cc_final: 0.7566 (mppt) REVERT: B 46 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7798 (pt0) outliers start: 22 outliers final: 10 residues processed: 96 average time/residue: 0.5741 time to fit residues: 57.6797 Evaluate side-chains 101 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 16 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 60 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN A 289 GLN B 71 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.182339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.140401 restraints weight = 5824.867| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.71 r_work: 0.3308 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6029 Z= 0.141 Angle : 0.525 5.664 8216 Z= 0.277 Chirality : 0.045 0.157 889 Planarity : 0.004 0.043 1072 Dihedral : 4.527 21.017 824 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.88 % Allowed : 13.20 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.29), residues: 748 helix: -2.45 (0.79), residues: 28 sheet: 0.28 (0.31), residues: 281 loop : -0.25 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 549 TYR 0.020 0.001 TYR A 548 PHE 0.011 0.001 PHE A 165 TRP 0.007 0.001 TRP A 515 HIS 0.003 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 6016) covalent geometry : angle 0.52407 / 0.28 ( 8190) SS BOND : bond 0.00289 / 0.15 ( 13) SS BOND : angle 0.77606 / 0.52 ( 26) hydrogen bonds : bond 0.02922 / 1.95 ( 203) hydrogen bonds : angle 5.72093 / 4.25 ( 507) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 THR cc_start: 0.7704 (p) cc_final: 0.7425 (t) REVERT: A 162 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8700 (ttt) REVERT: A 172 LYS cc_start: 0.8534 (ptpp) cc_final: 0.8242 (mttm) REVERT: A 185 LYS cc_start: 0.8130 (mtmm) cc_final: 0.7410 (mmtt) REVERT: A 254 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7130 (tmmm) REVERT: A 313 LEU cc_start: 0.8618 (mt) cc_final: 0.8406 (mm) REVERT: A 372 HIS cc_start: 0.8197 (t-90) cc_final: 0.7509 (m170) REVERT: A 392 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: A 453 MET cc_start: 0.5425 (OUTLIER) cc_final: 0.4199 (mpt) REVERT: A 457 MET cc_start: 0.6657 (OUTLIER) cc_final: 0.6438 (mpt) REVERT: A 541 LYS cc_start: 0.8626 (mttt) cc_final: 0.7875 (mmtm) REVERT: A 671 LYS cc_start: 0.8337 (ttpp) cc_final: 0.7618 (mppt) REVERT: B 46 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7971 (pt0) outliers start: 25 outliers final: 8 residues processed: 99 average time/residue: 0.5977 time to fit residues: 61.7300 Evaluate side-chains 98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 13 optimal weight: 0.0770 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN A 289 GLN A 429 HIS B 71 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.182594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.141347 restraints weight = 5757.095| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.77 r_work: 0.3345 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6029 Z= 0.134 Angle : 0.523 5.784 8216 Z= 0.276 Chirality : 0.045 0.155 889 Planarity : 0.004 0.040 1072 Dihedral : 4.494 22.115 824 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.42 % Allowed : 13.98 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.29), residues: 748 helix: -2.44 (0.80), residues: 28 sheet: 0.29 (0.31), residues: 281 loop : -0.23 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 549 TYR 0.020 0.001 TYR A 548 PHE 0.011 0.001 PHE A 165 TRP 0.007 0.001 TRP A 515 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 ( 6016) covalent geometry : angle 0.52275 / 0.28 ( 8190) SS BOND : bond 0.00266 / 0.14 ( 13) SS BOND : angle 0.71358 / 0.49 ( 26) hydrogen bonds : bond 0.02868 / 1.91 ( 203) hydrogen bonds : angle 5.66285 / 4.22 ( 507) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 THR cc_start: 0.7778 (p) cc_final: 0.7488 (t) REVERT: A 162 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8646 (ttt) REVERT: A 172 LYS cc_start: 0.8501 (ptpp) cc_final: 0.8224 (mttm) REVERT: A 185 LYS cc_start: 0.8097 (mtmm) cc_final: 0.7395 (mmtt) REVERT: A 254 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7150 (tmmm) REVERT: A 372 HIS cc_start: 0.8106 (t-90) cc_final: 0.7489 (m170) REVERT: A 392 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8133 (tt0) REVERT: A 453 MET cc_start: 0.5441 (OUTLIER) cc_final: 0.4223 (mpt) REVERT: A 541 LYS cc_start: 0.8597 (mttt) cc_final: 0.7857 (mmtm) REVERT: A 600 ASP cc_start: 0.9056 (OUTLIER) cc_final: 0.8614 (m-30) REVERT: A 671 LYS cc_start: 0.8295 (ttpp) cc_final: 0.7599 (mppt) REVERT: B 46 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7899 (pt0) outliers start: 22 outliers final: 8 residues processed: 98 average time/residue: 0.5911 time to fit residues: 60.5425 Evaluate side-chains 98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 0.0000 chunk 38 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN A 289 GLN A 347 GLN A 678 GLN B 71 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.183290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.141688 restraints weight = 5850.559| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.75 r_work: 0.3350 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6029 Z= 0.120 Angle : 0.511 5.987 8216 Z= 0.270 Chirality : 0.045 0.153 889 Planarity : 0.004 0.039 1072 Dihedral : 4.430 22.152 824 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.80 % Allowed : 15.22 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.29), residues: 748 helix: -2.40 (0.80), residues: 28 sheet: 0.30 (0.31), residues: 281 loop : -0.20 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 549 TYR 0.019 0.001 TYR A 548 PHE 0.011 0.001 PHE A 165 TRP 0.006 0.001 TRP A 515 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 6016) covalent geometry : angle 0.51055 / 0.27 ( 8190) SS BOND : bond 0.00237 / 0.12 ( 13) SS BOND : angle 0.65588 / 0.46 ( 26) hydrogen bonds : bond 0.02768 / 1.85 ( 203) hydrogen bonds : angle 5.58093 / 4.16 ( 507) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 THR cc_start: 0.7776 (p) cc_final: 0.7479 (t) REVERT: A 162 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8637 (ttt) REVERT: A 172 LYS cc_start: 0.8471 (ptpp) cc_final: 0.8184 (mttm) REVERT: A 185 LYS cc_start: 0.8010 (mtmm) cc_final: 0.7284 (mmtt) REVERT: A 243 ARG cc_start: 0.8276 (mmt-90) cc_final: 0.8034 (mmt-90) REVERT: A 254 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7014 (tmmm) REVERT: A 372 HIS cc_start: 0.8118 (t-90) cc_final: 0.7478 (m170) REVERT: A 385 THR cc_start: 0.8592 (m) cc_final: 0.8349 (t) REVERT: A 392 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8124 (tt0) REVERT: A 541 LYS cc_start: 0.8607 (mttt) cc_final: 0.7870 (mmtm) REVERT: A 600 ASP cc_start: 0.9056 (OUTLIER) cc_final: 0.8619 (m-30) REVERT: A 671 LYS cc_start: 0.8304 (ttpp) cc_final: 0.7608 (mppt) REVERT: B 46 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7888 (pt0) outliers start: 18 outliers final: 8 residues processed: 96 average time/residue: 0.5894 time to fit residues: 59.1562 Evaluate side-chains 98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 30 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN A 289 GLN A 347 GLN B 71 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.182675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.140676 restraints weight = 5795.443| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.77 r_work: 0.3334 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6029 Z= 0.138 Angle : 0.530 6.156 8216 Z= 0.279 Chirality : 0.045 0.155 889 Planarity : 0.004 0.039 1072 Dihedral : 4.496 22.032 824 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.80 % Allowed : 15.22 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.29), residues: 748 helix: -2.50 (0.78), residues: 28 sheet: 0.33 (0.31), residues: 280 loop : -0.23 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 549 TYR 0.021 0.001 TYR A 548 PHE 0.011 0.001 PHE A 165 TRP 0.006 0.001 TRP A 515 HIS 0.004 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 6016) covalent geometry : angle 0.52935 / 0.28 ( 8190) SS BOND : bond 0.00269 / 0.14 ( 13) SS BOND : angle 0.69021 / 0.49 ( 26) hydrogen bonds : bond 0.02828 / 1.89 ( 203) hydrogen bonds : angle 5.61061 / 4.19 ( 507) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 THR cc_start: 0.7823 (p) cc_final: 0.7522 (t) REVERT: A 162 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8698 (ttt) REVERT: A 172 LYS cc_start: 0.8496 (ptpp) cc_final: 0.8228 (mttm) REVERT: A 185 LYS cc_start: 0.7930 (mtmm) cc_final: 0.7260 (mmtt) REVERT: A 254 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7146 (tmmm) REVERT: A 372 HIS cc_start: 0.8152 (t-90) cc_final: 0.7494 (m170) REVERT: A 385 THR cc_start: 0.8600 (m) cc_final: 0.8359 (t) REVERT: A 392 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8132 (tt0) REVERT: A 541 LYS cc_start: 0.8638 (mttt) cc_final: 0.7903 (mmtm) REVERT: A 600 ASP cc_start: 0.9053 (OUTLIER) cc_final: 0.8613 (m-30) REVERT: A 671 LYS cc_start: 0.8297 (ttpp) cc_final: 0.7598 (mppt) REVERT: B 46 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7952 (pt0) outliers start: 18 outliers final: 10 residues processed: 95 average time/residue: 0.5966 time to fit residues: 59.3581 Evaluate side-chains 100 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 61 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 39 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN A 289 GLN B 71 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.183074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.140526 restraints weight = 5740.907| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.70 r_work: 0.3326 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6029 Z= 0.131 Angle : 0.520 6.237 8216 Z= 0.274 Chirality : 0.045 0.154 889 Planarity : 0.004 0.039 1072 Dihedral : 4.463 22.364 824 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.80 % Allowed : 15.53 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.29), residues: 748 helix: -2.51 (0.77), residues: 28 sheet: 0.30 (0.31), residues: 281 loop : -0.20 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 549 TYR 0.021 0.001 TYR A 548 PHE 0.011 0.001 PHE A 165 TRP 0.006 0.001 TRP A 515 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 6016) covalent geometry : angle 0.51997 / 0.27 ( 8190) SS BOND : bond 0.00256 / 0.13 ( 13) SS BOND : angle 0.66690 / 0.47 ( 26) hydrogen bonds : bond 0.02785 / 1.86 ( 203) hydrogen bonds : angle 5.55549 / 4.14 ( 507) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2375.42 seconds wall clock time: 41 minutes 14.68 seconds (2474.68 seconds total)