Starting phenix.real_space_refine on Thu Mar 5 00:35:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t8t_25745/03_2026/7t8t_25745.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t8t_25745/03_2026/7t8t_25745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t8t_25745/03_2026/7t8t_25745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t8t_25745/03_2026/7t8t_25745.map" model { file = "/net/cci-nas-00/data/ceres_data/7t8t_25745/03_2026/7t8t_25745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t8t_25745/03_2026/7t8t_25745.cif" } resolution = 3.68 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= 0.015 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 S 49 5.16 5 C 5595 2.51 5 N 1517 2.21 5 O 1646 1.98 5 H 8626 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17434 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 17433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 17433 Classifications: {'peptide': 1086} Link IDs: {'PTRANS': 56, 'TRANS': 1029} Chain breaks: 5 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.18, per 1000 atoms: 0.18 Number of scatterers: 17434 At special positions: 0 Unit cell: (86.45, 103.74, 111.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 49 16.00 O 1646 8.00 N 1517 7.00 C 5595 6.00 H 8626 1.00 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: 1.63 Conformation dependent library (CDL) restraints added in 656.5 milliseconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 11 sheets defined 30.5% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 22 through 32 removed outlier: 4.166A pdb=" N GLY A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 95 removed outlier: 4.328A pdb=" N GLU A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 146 removed outlier: 3.848A pdb=" N GLN A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 163 Processing helix chain 'A' and resid 173 through 183 Processing helix chain 'A' and resid 209 through 224 Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.666A pdb=" N PHE A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 269 through 282 removed outlier: 3.538A pdb=" N VAL A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 304 removed outlier: 3.811A pdb=" N PHE A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 308 Processing helix chain 'A' and resid 311 through 316 removed outlier: 3.828A pdb=" N ALA A 316 " --> pdb=" O GLN A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 322 Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 349 through 360 removed outlier: 4.165A pdb=" N TYR A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY A 360 " --> pdb=" O CYS A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 419 through 434 Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 451 through 456 removed outlier: 3.725A pdb=" N LYS A 456 " --> pdb=" O ASN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 548 Processing helix chain 'A' and resid 558 through 568 removed outlier: 4.565A pdb=" N GLU A 566 " --> pdb=" O ARG A 562 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 567 " --> pdb=" O HIS A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 574 removed outlier: 3.869A pdb=" N ILE A 574 " --> pdb=" O THR A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 639 removed outlier: 4.070A pdb=" N TYR A 639 " --> pdb=" O LEU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.737A pdb=" N VAL A 685 " --> pdb=" O MET A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 743 removed outlier: 3.584A pdb=" N LYS A 743 " --> pdb=" O SER A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 763 Processing helix chain 'A' and resid 879 through 881 No H-bonds generated for 'chain 'A' and resid 879 through 881' Processing helix chain 'A' and resid 915 through 931 removed outlier: 3.605A pdb=" N LEU A 919 " --> pdb=" O SER A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 957 removed outlier: 3.549A pdb=" N SER A 954 " --> pdb=" O ALA A 950 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 956 " --> pdb=" O GLU A 952 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL A 957 " --> pdb=" O LEU A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 990 removed outlier: 3.736A pdb=" N LYS A 990 " --> pdb=" O THR A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1005 removed outlier: 4.679A pdb=" N LYS A 998 " --> pdb=" O LYS A 994 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LYS A 999 " --> pdb=" O ALA A 995 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN A1002 " --> pdb=" O LYS A 998 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A1004 " --> pdb=" O PHE A1000 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1032 Processing helix chain 'A' and resid 1044 through 1054 removed outlier: 3.771A pdb=" N PHE A1054 " --> pdb=" O ASN A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1071 Processing helix chain 'A' and resid 1078 through 1083 removed outlier: 3.519A pdb=" N ARG A1083 " --> pdb=" O SER A1080 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 74 removed outlier: 3.739A pdb=" N THR A 50 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER A 121 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N CYS A 106 " --> pdb=" O PRO A 83 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL A 108 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ILE A 81 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU A 110 " --> pdb=" O LYS A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 249 removed outlier: 3.767A pdb=" N PHE A 293 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 377 through 378 removed outlier: 6.445A pdb=" N ILE A 364 " --> pdb=" O SER A 412 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N GLU A 414 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU A 366 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL A 409 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LYS A 462 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU A 411 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 491 through 497 removed outlier: 3.627A pdb=" N LYS A 491 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TYR A 509 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR A 519 " --> pdb=" O GLY A 874 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 583 through 587 removed outlier: 3.858A pdb=" N PHE A 599 " --> pdb=" O GLN A 606 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 610 through 611 Processing sheet with id=AA7, first strand: chain 'A' and resid 723 through 725 removed outlier: 4.673A pdb=" N ALA A 690 " --> pdb=" O ARG A 707 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 882 through 883 Processing sheet with id=AA9, first strand: chain 'A' and resid 982 through 983 Processing sheet with id=AB1, first strand: chain 'A' and resid 1145 through 1149 removed outlier: 7.027A pdb=" N LEU A1206 " --> pdb=" O LEU A1095 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ALA A1097 " --> pdb=" O SER A1204 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER A1204 " --> pdb=" O ALA A1097 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1124 through 1127 removed outlier: 3.823A pdb=" N ALA A1174 " --> pdb=" O VAL A1161 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLU A1163 " --> pdb=" O PHE A1172 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N PHE A1172 " --> pdb=" O GLU A1163 " (cutoff:3.500A) 274 hydrogen bonds defined for protein. 726 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.08 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8606 1.03 - 1.23: 21 1.23 - 1.42: 3836 1.42 - 1.61: 5098 1.61 - 1.81: 78 Bond restraints: 17639 Sorted by residual: bond pdb=" CB TRP A 668 " pdb=" CG TRP A 668 " ideal model delta sigma weight residual 1.498 1.529 -0.031 3.10e-02 1.04e+03 1.02e+00 bond pdb=" CA PRO A 984 " pdb=" C PRO A 984 " ideal model delta sigma weight residual 1.520 1.532 -0.013 1.42e-02 4.96e+03 7.82e-01 bond pdb=" C GLU A 768 " pdb=" N PRO A 769 " ideal model delta sigma weight residual 1.326 1.338 -0.012 1.44e-02 4.82e+03 7.14e-01 bond pdb=" CA PRO A 984 " pdb=" CB PRO A 984 " ideal model delta sigma weight residual 1.533 1.522 0.012 1.42e-02 4.96e+03 6.73e-01 bond pdb=" C PHE A 983 " pdb=" N PRO A 984 " ideal model delta sigma weight residual 1.334 1.352 -0.018 2.34e-02 1.83e+03 6.20e-01 ... (remaining 17634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 31264 1.46 - 2.92: 509 2.92 - 4.39: 54 4.39 - 5.85: 3 5.85 - 7.31: 1 Bond angle restraints: 31831 Sorted by residual: angle pdb=" N VAL A 164 " pdb=" CA VAL A 164 " pdb=" C VAL A 164 " ideal model delta sigma weight residual 111.91 108.73 3.18 8.90e-01 1.26e+00 1.27e+01 angle pdb=" CB ARG A 423 " pdb=" CG ARG A 423 " pdb=" CD ARG A 423 " ideal model delta sigma weight residual 111.30 118.61 -7.31 2.30e+00 1.89e-01 1.01e+01 angle pdb=" N ASP A1122 " pdb=" CA ASP A1122 " pdb=" C ASP A1122 " ideal model delta sigma weight residual 114.04 110.53 3.51 1.24e+00 6.50e-01 8.00e+00 angle pdb=" C GLU A 474 " pdb=" N VAL A 475 " pdb=" CA VAL A 475 " ideal model delta sigma weight residual 122.13 127.31 -5.18 1.85e+00 2.92e-01 7.83e+00 angle pdb=" N ARG A 423 " pdb=" CA ARG A 423 " pdb=" CB ARG A 423 " ideal model delta sigma weight residual 110.12 114.01 -3.89 1.47e+00 4.63e-01 7.00e+00 ... (remaining 31826 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 7550 17.19 - 34.38: 582 34.38 - 51.58: 155 51.58 - 68.77: 36 68.77 - 85.96: 9 Dihedral angle restraints: 8332 sinusoidal: 4520 harmonic: 3812 Sorted by residual: dihedral pdb=" CA LEU A 194 " pdb=" C LEU A 194 " pdb=" N ARG A 195 " pdb=" CA ARG A 195 " ideal model delta harmonic sigma weight residual -180.00 -163.33 -16.67 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ARG A 945 " pdb=" C ARG A 945 " pdb=" N ARG A 946 " pdb=" CA ARG A 946 " ideal model delta harmonic sigma weight residual -180.00 -163.58 -16.42 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA GLU A 289 " pdb=" C GLU A 289 " pdb=" N GLU A 290 " pdb=" CA GLU A 290 " ideal model delta harmonic sigma weight residual 180.00 163.90 16.10 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 8329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 910 0.032 - 0.065: 267 0.065 - 0.097: 72 0.097 - 0.129: 56 0.129 - 0.162: 2 Chirality restraints: 1307 Sorted by residual: chirality pdb=" CB ILE A 419 " pdb=" CA ILE A 419 " pdb=" CG1 ILE A 419 " pdb=" CG2 ILE A 419 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA ILE A 109 " pdb=" N ILE A 109 " pdb=" C ILE A 109 " pdb=" CB ILE A 109 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE A1011 " pdb=" N ILE A1011 " pdb=" C ILE A1011 " pdb=" CB ILE A1011 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 1304 not shown) Planarity restraints: 2609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 985 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.94e+00 pdb=" C GLU A 985 " 0.038 2.00e-02 2.50e+03 pdb=" O GLU A 985 " -0.014 2.00e-02 2.50e+03 pdb=" N THR A 986 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 668 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.15e+00 pdb=" C TRP A 668 " 0.025 2.00e-02 2.50e+03 pdb=" O TRP A 668 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR A 669 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 423 " 0.097 9.50e-02 1.11e+02 3.27e-02 1.71e+00 pdb=" NE ARG A 423 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 423 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 423 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 423 " -0.003 2.00e-02 2.50e+03 pdb="HH11 ARG A 423 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG A 423 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 423 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 423 " 0.001 2.00e-02 2.50e+03 ... (remaining 2606 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1151 2.20 - 2.80: 35642 2.80 - 3.40: 44872 3.40 - 4.00: 58252 4.00 - 4.60: 88840 Nonbonded interactions: 228757 Sorted by model distance: nonbonded pdb=" OD1 ASP A 342 " pdb=" HG SER A 346 " model vdw 1.602 2.450 nonbonded pdb=" H SER A 588 " pdb=" O ASP A 594 " model vdw 1.616 2.450 nonbonded pdb=" OD1 ASN A 993 " pdb=" H LYS A 996 " model vdw 1.618 2.450 nonbonded pdb=" OD1 ASP A1165 " pdb=" H ASP A1169 " model vdw 1.619 2.450 nonbonded pdb=" HG SER A 915 " pdb=" OE1 GLU A 918 " model vdw 1.621 2.450 ... (remaining 228752 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 group one per residue 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: 2.250 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: 0.090 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.190 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 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 : 0.002 0.031 9013 Z= 0.105 Angle : 0.500 7.309 12185 Z= 0.270 Chirality : 0.039 0.162 1307 Planarity : 0.003 0.042 1584 Dihedral : 13.832 85.961 3402 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.68 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.27), residues: 1074 helix: 1.32 (0.35), residues: 264 sheet: -0.66 (0.35), residues: 231 loop : -1.40 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 423 TYR 0.006 0.001 TYR A1012 PHE 0.014 0.001 PHE A 254 TRP 0.014 0.001 TRP A 550 HIS 0.002 0.000 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 9013) covalent geometry : angle 0.50040 (12185) hydrogen bonds : bond 0.16677 ( 274) hydrogen bonds : angle 6.07426 ( 726) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 620 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1565 time to fit residues: 16.9153 Evaluate side-chains 62 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0870 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN A 503 HIS ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.125289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.089457 restraints weight = 57284.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.093766 restraints weight = 24665.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.096370 restraints weight = 15196.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.097908 restraints weight = 11545.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.098770 restraints weight = 9884.555| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9013 Z= 0.187 Angle : 0.544 5.429 12185 Z= 0.286 Chirality : 0.040 0.143 1307 Planarity : 0.004 0.047 1584 Dihedral : 4.205 17.576 1193 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.66 % Favored : 91.15 % Rotamer: Outliers : 0.31 % Allowed : 3.52 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.26), residues: 1074 helix: 1.06 (0.34), residues: 268 sheet: -0.77 (0.34), residues: 227 loop : -1.71 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 197 TYR 0.008 0.001 TYR A 519 PHE 0.015 0.002 PHE A 983 TRP 0.008 0.001 TRP A 550 HIS 0.003 0.001 HIS A 663 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 9013) covalent geometry : angle 0.54440 (12185) hydrogen bonds : bond 0.03991 ( 274) hydrogen bonds : angle 5.26344 ( 726) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 620 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.8150 (tmtt) cc_final: 0.7855 (ptpt) REVERT: A 571 GLU cc_start: 0.8660 (mp0) cc_final: 0.8391 (pm20) outliers start: 3 outliers final: 2 residues processed: 59 average time/residue: 0.1784 time to fit residues: 15.8928 Evaluate side-chains 55 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 1163 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 37 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 chunk 59 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 HIS A 545 HIS ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.123887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.087996 restraints weight = 57685.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.092267 restraints weight = 24811.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.094874 restraints weight = 15337.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.096429 restraints weight = 11654.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.097341 restraints weight = 9951.583| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9013 Z= 0.179 Angle : 0.531 5.293 12185 Z= 0.280 Chirality : 0.040 0.143 1307 Planarity : 0.004 0.062 1584 Dihedral : 4.362 17.547 1193 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.75 % Favored : 91.06 % Rotamer: Outliers : 0.52 % Allowed : 5.28 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.26), residues: 1074 helix: 0.89 (0.34), residues: 275 sheet: -1.03 (0.33), residues: 233 loop : -1.78 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 197 TYR 0.012 0.001 TYR A 754 PHE 0.014 0.002 PHE A1000 TRP 0.006 0.001 TRP A1140 HIS 0.005 0.001 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 9013) covalent geometry : angle 0.53111 (12185) hydrogen bonds : bond 0.04238 ( 274) hydrogen bonds : angle 5.13714 ( 726) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 620 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.8120 (tmtt) cc_final: 0.7900 (ptpt) REVERT: A 571 GLU cc_start: 0.8727 (mp0) cc_final: 0.8479 (pm20) REVERT: A 651 MET cc_start: 0.4125 (mmp) cc_final: 0.3925 (mmp) outliers start: 5 outliers final: 3 residues processed: 63 average time/residue: 0.1905 time to fit residues: 17.6437 Evaluate side-chains 59 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1163 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 98 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 30 optimal weight: 0.0980 chunk 79 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.124582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.088430 restraints weight = 57226.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.092737 restraints weight = 24765.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.095338 restraints weight = 15321.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.096896 restraints weight = 11647.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.097819 restraints weight = 9980.748| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9013 Z= 0.131 Angle : 0.501 7.582 12185 Z= 0.260 Chirality : 0.039 0.140 1307 Planarity : 0.004 0.064 1584 Dihedral : 4.230 17.426 1193 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.19 % Favored : 91.62 % Rotamer: Outliers : 0.41 % Allowed : 7.14 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.26), residues: 1074 helix: 1.06 (0.34), residues: 275 sheet: -1.04 (0.33), residues: 235 loop : -1.71 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 197 TYR 0.011 0.001 TYR A 519 PHE 0.013 0.001 PHE A 276 TRP 0.005 0.001 TRP A1140 HIS 0.004 0.001 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9013) covalent geometry : angle 0.50090 (12185) hydrogen bonds : bond 0.03435 ( 274) hydrogen bonds : angle 4.87887 ( 726) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 620 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.8186 (tmtt) cc_final: 0.7970 (ptpt) REVERT: A 571 GLU cc_start: 0.8767 (mp0) cc_final: 0.8560 (pm20) REVERT: A 651 MET cc_start: 0.3902 (mmp) cc_final: 0.3549 (mmp) outliers start: 4 outliers final: 3 residues processed: 63 average time/residue: 0.1767 time to fit residues: 16.5539 Evaluate side-chains 59 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1163 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 95 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 59 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.123876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.087723 restraints weight = 57531.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.092025 restraints weight = 24762.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.094597 restraints weight = 15307.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.096137 restraints weight = 11690.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.096918 restraints weight = 10000.401| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9013 Z= 0.149 Angle : 0.506 6.188 12185 Z= 0.264 Chirality : 0.039 0.141 1307 Planarity : 0.004 0.064 1584 Dihedral : 4.265 17.447 1193 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.75 % Favored : 91.06 % Rotamer: Outliers : 0.41 % Allowed : 8.07 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.27), residues: 1074 helix: 1.18 (0.35), residues: 269 sheet: -1.12 (0.33), residues: 235 loop : -1.70 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 197 TYR 0.012 0.001 TYR A 519 PHE 0.013 0.001 PHE A 276 TRP 0.007 0.001 TRP A 668 HIS 0.004 0.001 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9013) covalent geometry : angle 0.50552 (12185) hydrogen bonds : bond 0.03555 ( 274) hydrogen bonds : angle 4.86328 ( 726) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 620 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 571 GLU cc_start: 0.8773 (mp0) cc_final: 0.8538 (pm20) REVERT: A 651 MET cc_start: 0.3949 (mmp) cc_final: 0.3624 (mmp) outliers start: 4 outliers final: 3 residues processed: 63 average time/residue: 0.1727 time to fit residues: 16.5905 Evaluate side-chains 60 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1113 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 7 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.123284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.087232 restraints weight = 57113.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.091448 restraints weight = 24717.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.093993 restraints weight = 15344.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.095533 restraints weight = 11755.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.096303 restraints weight = 10024.077| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9013 Z= 0.172 Angle : 0.528 6.734 12185 Z= 0.276 Chirality : 0.040 0.142 1307 Planarity : 0.004 0.067 1584 Dihedral : 4.369 18.346 1193 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.22 % Favored : 90.60 % Rotamer: Outliers : 0.62 % Allowed : 8.59 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.26), residues: 1074 helix: 1.06 (0.34), residues: 269 sheet: -1.18 (0.34), residues: 230 loop : -1.81 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 197 TYR 0.012 0.001 TYR A 519 PHE 0.014 0.001 PHE A 276 TRP 0.007 0.001 TRP A1140 HIS 0.004 0.001 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9013) covalent geometry : angle 0.52793 (12185) hydrogen bonds : bond 0.03707 ( 274) hydrogen bonds : angle 4.93260 ( 726) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 620 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.7937 (tptt) cc_final: 0.7718 (pttt) REVERT: A 571 GLU cc_start: 0.8775 (mp0) cc_final: 0.8542 (pm20) REVERT: A 651 MET cc_start: 0.3465 (mmp) cc_final: 0.3114 (mmp) outliers start: 6 outliers final: 5 residues processed: 65 average time/residue: 0.1744 time to fit residues: 16.8881 Evaluate side-chains 61 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1113 GLU Chi-restraints excluded: chain A residue 1163 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 30 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.125141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.088950 restraints weight = 56894.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.093343 restraints weight = 24281.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.096003 restraints weight = 14903.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.097580 restraints weight = 11327.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.098385 restraints weight = 9676.623| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9013 Z= 0.092 Angle : 0.478 7.117 12185 Z= 0.247 Chirality : 0.039 0.136 1307 Planarity : 0.004 0.068 1584 Dihedral : 4.101 17.102 1193 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.70 % Favored : 93.11 % Rotamer: Outliers : 0.41 % Allowed : 9.01 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.27), residues: 1074 helix: 1.23 (0.34), residues: 275 sheet: -1.10 (0.34), residues: 235 loop : -1.64 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 76 TYR 0.011 0.001 TYR A 519 PHE 0.009 0.001 PHE A 276 TRP 0.008 0.001 TRP A 668 HIS 0.003 0.001 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 9013) covalent geometry : angle 0.47844 (12185) hydrogen bonds : bond 0.02942 ( 274) hydrogen bonds : angle 4.60171 ( 726) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 620 is missing expected H atoms. Skipping. Evaluate side-chains 64 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.8040 (tptt) cc_final: 0.7764 (pttt) REVERT: A 651 MET cc_start: 0.3408 (mmp) cc_final: 0.3066 (mmp) outliers start: 4 outliers final: 4 residues processed: 64 average time/residue: 0.1776 time to fit residues: 16.7540 Evaluate side-chains 61 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1163 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 13 optimal weight: 0.0010 chunk 47 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 77 optimal weight: 0.1980 chunk 8 optimal weight: 3.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.125103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.089106 restraints weight = 56751.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.093431 restraints weight = 24348.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.096065 restraints weight = 14975.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.097617 restraints weight = 11375.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.098403 restraints weight = 9699.398| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9013 Z= 0.101 Angle : 0.482 7.322 12185 Z= 0.248 Chirality : 0.039 0.137 1307 Planarity : 0.004 0.068 1584 Dihedral : 4.042 17.207 1193 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.45 % Favored : 92.36 % Rotamer: Outliers : 0.62 % Allowed : 9.01 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.27), residues: 1074 helix: 1.29 (0.34), residues: 275 sheet: -1.12 (0.34), residues: 227 loop : -1.60 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 197 TYR 0.012 0.001 TYR A 519 PHE 0.009 0.001 PHE A 276 TRP 0.006 0.001 TRP A 668 HIS 0.003 0.001 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9013) covalent geometry : angle 0.48194 (12185) hydrogen bonds : bond 0.02937 ( 274) hydrogen bonds : angle 4.57079 ( 726) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 620 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.8007 (tptt) cc_final: 0.7769 (pttt) outliers start: 6 outliers final: 5 residues processed: 65 average time/residue: 0.1967 time to fit residues: 18.3804 Evaluate side-chains 63 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1163 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 57 optimal weight: 30.0000 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.124008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.087932 restraints weight = 57388.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.092254 restraints weight = 24551.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.094849 restraints weight = 15109.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.096344 restraints weight = 11465.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.097080 restraints weight = 9847.416| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9013 Z= 0.137 Angle : 0.503 7.203 12185 Z= 0.261 Chirality : 0.039 0.140 1307 Planarity : 0.004 0.070 1584 Dihedral : 4.179 17.136 1193 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.22 % Favored : 90.60 % Rotamer: Outliers : 0.62 % Allowed : 9.11 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.27), residues: 1074 helix: 1.37 (0.35), residues: 269 sheet: -1.02 (0.35), residues: 221 loop : -1.69 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 197 TYR 0.013 0.001 TYR A 519 PHE 0.012 0.001 PHE A 276 TRP 0.006 0.001 TRP A1140 HIS 0.004 0.001 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9013) covalent geometry : angle 0.50277 (12185) hydrogen bonds : bond 0.03308 ( 274) hydrogen bonds : angle 4.66411 ( 726) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 620 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.7960 (tptt) cc_final: 0.7758 (pttt) REVERT: A 651 MET cc_start: 0.3479 (mmp) cc_final: 0.3166 (mmp) outliers start: 6 outliers final: 5 residues processed: 63 average time/residue: 0.1690 time to fit residues: 16.2256 Evaluate side-chains 60 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1113 GLU Chi-restraints excluded: chain A residue 1163 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 15 optimal weight: 3.9990 chunk 72 optimal weight: 0.0970 chunk 53 optimal weight: 4.9990 chunk 6 optimal weight: 0.0370 chunk 24 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.125781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.090010 restraints weight = 56152.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.094367 restraints weight = 23964.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.097016 restraints weight = 14765.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.098574 restraints weight = 11187.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.099317 restraints weight = 9579.613| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9013 Z= 0.082 Angle : 0.478 7.160 12185 Z= 0.245 Chirality : 0.039 0.136 1307 Planarity : 0.004 0.071 1584 Dihedral : 3.954 16.990 1193 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.89 % Favored : 92.92 % Rotamer: Outliers : 0.41 % Allowed : 9.52 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.27), residues: 1074 helix: 1.37 (0.35), residues: 275 sheet: -0.98 (0.35), residues: 218 loop : -1.57 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 197 TYR 0.011 0.001 TYR A 572 PHE 0.007 0.001 PHE A 390 TRP 0.009 0.001 TRP A 668 HIS 0.004 0.001 HIS A 680 Details of bonding type rmsd covalent geometry : bond 0.00197 ( 9013) covalent geometry : angle 0.47813 (12185) hydrogen bonds : bond 0.02643 ( 274) hydrogen bonds : angle 4.43568 ( 726) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 163 is missing expected H atoms. Skipping. Residue LEU 544 is missing expected H atoms. Skipping. Residue LYS 620 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.8039 (tptt) cc_final: 0.7762 (pttt) outliers start: 4 outliers final: 4 residues processed: 66 average time/residue: 0.1880 time to fit residues: 18.1860 Evaluate side-chains 62 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1113 GLU Chi-restraints excluded: chain A residue 1163 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 47 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 9 optimal weight: 0.0970 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 0.0870 chunk 82 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.125538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.089652 restraints weight = 56821.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.094028 restraints weight = 24130.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.096671 restraints weight = 14783.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.098229 restraints weight = 11176.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.098930 restraints weight = 9560.264| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9013 Z= 0.090 Angle : 0.476 7.142 12185 Z= 0.243 Chirality : 0.039 0.135 1307 Planarity : 0.004 0.071 1584 Dihedral : 3.925 17.012 1193 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.45 % Favored : 92.36 % Rotamer: Outliers : 0.52 % Allowed : 9.52 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.27), residues: 1074 helix: 1.41 (0.35), residues: 275 sheet: -0.87 (0.35), residues: 226 loop : -1.58 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 197 TYR 0.011 0.001 TYR A 572 PHE 0.008 0.001 PHE A1111 TRP 0.006 0.001 TRP A 668 HIS 0.003 0.000 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 9013) covalent geometry : angle 0.47558 (12185) hydrogen bonds : bond 0.02722 ( 274) hydrogen bonds : angle 4.41854 ( 726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2901.47 seconds wall clock time: 49 minutes 58.15 seconds (2998.15 seconds total)