Starting phenix.real_space_refine on Mon Jan 20 01:07:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9der_46794/01_2025/9der_46794_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9der_46794/01_2025/9der_46794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9der_46794/01_2025/9der_46794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9der_46794/01_2025/9der_46794.map" model { file = "/net/cci-nas-00/data/ceres_data/9der_46794/01_2025/9der_46794_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9der_46794/01_2025/9der_46794_trim.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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: 7 Type Number sf(0) Gaussians Ca 6 9.91 5 Mg 1 5.21 5 S 44 5.16 5 C 4612 2.51 5 N 1232 2.21 5 O 1469 1.98 5 H 6843 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 14207 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 6697 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 26, 'TRANS': 421} Chain: "B" Number of atoms: 7265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 7265 Classifications: {'peptide': 477} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 24, 'TRANS': 449} Chain breaks: 1 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 35 Unusual residues: {' CA': 2, ' MG': 1} Classifications: {'peptide': 1, 'undetermined': 3, 'water': 2} Link IDs: {None: 5} Time building chain proxies: 7.54, per 1000 atoms: 0.53 Number of scatterers: 14207 At special positions: 0 Unit cell: (82.08, 101.52, 166.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 6 19.99 S 44 16.00 Mg 1 11.99 O 1469 8.00 N 1232 7.00 C 4612 6.00 H 6843 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 167 " distance=2.03 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 23 " distance=2.03 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 435 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 38 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 406 " - pdb=" SG CYS B 433 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 448 " - pdb=" SG CYS B 460 " distance=2.03 Simple disulfide: pdb=" SG CYS B 460 " - pdb=" SG CYS B 471 " distance=2.03 Simple disulfide: pdb=" SG CYS B 462 " - pdb=" SG CYS B 471 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " BMA E 3 " - " BMA E 4 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " BETA1-6 " BMA D 3 " - " BMA D 4 " NAG-ASN " NAG C 1 " - " ASN A 249 " " NAG D 1 " - " ASN B 320 " " NAG E 1 " - " ASN A 15 " " NAG F 1 " - " ASN B 371 " " NAG G 1 " - " ASN B 99 " Time building additional restraints: 4.77 Conformation dependent library (CDL) restraints added in 1.3 seconds 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1686 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 13 sheets defined 17.2% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 227 through 231 Processing helix chain 'B' and resid 12 through 19 Processing helix chain 'B' and resid 31 through 35 removed outlier: 3.982A pdb=" N GLY B 34 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 Processing helix chain 'B' and resid 123 through 146 removed outlier: 4.429A pdb=" N ASP B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TRP B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N SER B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 175 removed outlier: 4.141A pdb=" N GLU B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 210 Processing helix chain 'B' and resid 221 through 232 removed outlier: 3.799A pdb=" N ALA B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 removed outlier: 4.169A pdb=" N ALA B 263 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 287 removed outlier: 4.361A pdb=" N THR B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 303 Processing helix chain 'B' and resid 314 through 325 removed outlier: 3.779A pdb=" N TYR B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.900A pdb=" N LEU B 343 " --> pdb=" O ASN B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 441 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 11 Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 27 removed outlier: 3.634A pdb=" N SER A 22 " --> pdb=" O GLY A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 79 Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 100 removed outlier: 3.739A pdb=" N SER A 96 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 175 Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 242 removed outlier: 6.773A pdb=" N VAL A 267 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG A 279 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A 269 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 293 through 296 Processing sheet with id=AA8, first strand: chain 'A' and resid 314 through 315 Processing sheet with id=AA9, first strand: chain 'A' and resid 360 through 362 removed outlier: 3.565A pdb=" N GLN A 405 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 61 through 65 removed outlier: 6.252A pdb=" N ARG B 87 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 83 through 84 Processing sheet with id=AB3, first strand: chain 'B' and resid 190 through 197 removed outlier: 6.525A pdb=" N VAL B 193 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ALA B 155 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N THR B 195 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N PHE B 153 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP B 119 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR B 250 " --> pdb=" O ALA B 309 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 454 through 456 253 hydrogen bonds defined for protein. 660 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: 5.66 Time building geometry restraints manager: 5.23 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: 6841 1.03 - 1.23: 16 1.23 - 1.42: 3182 1.42 - 1.62: 4265 1.62 - 1.82: 59 Bond restraints: 14363 Sorted by residual: bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.558 -0.039 2.00e-02 2.50e+03 3.84e+00 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.554 -0.035 2.00e-02 2.50e+03 2.98e+00 bond pdb=" C1 BMA D 4 " pdb=" C2 BMA D 4 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C1 BMA E 4 " pdb=" C2 BMA E 4 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C1 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sigma weight residual 1.410 1.438 -0.028 2.00e-02 2.50e+03 2.03e+00 ... (remaining 14358 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.09: 25789 7.09 - 14.19: 1 14.19 - 21.28: 0 21.28 - 28.37: 0 28.37 - 35.46: 3 Bond angle restraints: 25793 Sorted by residual: angle pdb=" C LYS B 72 " pdb=" CA LYS B 72 " pdb=" HA LYS B 72 " ideal model delta sigma weight residual 109.00 73.54 35.46 3.00e+00 1.11e-01 1.40e+02 angle pdb=" N LYS B 72 " pdb=" CA LYS B 72 " pdb=" HA LYS B 72 " ideal model delta sigma weight residual 110.00 74.64 35.36 3.00e+00 1.11e-01 1.39e+02 angle pdb=" CB LYS B 72 " pdb=" CA LYS B 72 " pdb=" HA LYS B 72 " ideal model delta sigma weight residual 109.00 79.83 29.17 3.00e+00 1.11e-01 9.45e+01 angle pdb=" N LYS B 72 " pdb=" CA LYS B 72 " pdb=" C LYS B 72 " ideal model delta sigma weight residual 111.00 121.57 -10.57 2.80e+00 1.28e-01 1.43e+01 angle pdb=" C3 BMA D 3 " pdb=" C2 BMA D 3 " pdb=" O2 BMA D 3 " ideal model delta sigma weight residual 112.95 106.60 6.35 3.00e+00 1.11e-01 4.48e+00 ... (remaining 25788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.77: 6756 22.77 - 45.53: 230 45.53 - 68.30: 70 68.30 - 91.07: 38 91.07 - 113.84: 24 Dihedral angle restraints: 7118 sinusoidal: 4024 harmonic: 3094 Sorted by residual: dihedral pdb=" CB CYS B 16 " pdb=" SG CYS B 16 " pdb=" SG CYS B 38 " pdb=" CB CYS B 38 " ideal model delta sinusoidal sigma weight residual -86.00 -132.89 46.89 1 1.00e+01 1.00e-02 3.04e+01 dihedral pdb=" CB CYS B 448 " pdb=" SG CYS B 448 " pdb=" SG CYS B 460 " pdb=" CB CYS B 460 " ideal model delta sinusoidal sigma weight residual 93.00 128.55 -35.55 1 1.00e+01 1.00e-02 1.79e+01 dihedral pdb=" O4 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C5 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sinusoidal sigma weight residual 288.71 174.87 113.84 1 3.00e+01 1.11e-03 1.50e+01 ... (remaining 7115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1066 0.093 - 0.187: 82 0.187 - 0.280: 7 0.280 - 0.374: 2 0.374 - 0.467: 2 Chirality restraints: 1159 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 249 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" CA LYS B 72 " pdb=" N LYS B 72 " pdb=" C LYS B 72 " pdb=" CB LYS B 72 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.46 2.00e-01 2.50e+01 5.18e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 1156 not shown) Planarity restraints: 2194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 380 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO B 381 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 381 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 381 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 93 " 0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO B 94 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO B 94 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 94 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 336 " 0.017 5.00e-02 4.00e+02 2.53e-02 1.03e+00 pdb=" N PRO A 337 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " 0.014 5.00e-02 4.00e+02 ... (remaining 2191 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 564 2.17 - 2.78: 27587 2.78 - 3.38: 38070 3.38 - 3.99: 49374 3.99 - 4.60: 76502 Nonbonded interactions: 192097 Sorted by model distance: nonbonded pdb=" O GLN B 267 " pdb=" H ASP B 288 " model vdw 1.560 2.450 nonbonded pdb=" OD1 ASP B 158 " pdb=" H LYS B 159 " model vdw 1.622 2.450 nonbonded pdb=" O GLU B 356 " pdb=" H VAL B 419 " model vdw 1.626 2.450 nonbonded pdb=" H ILE B 256 " pdb=" OD2 ASP B 259 " model vdw 1.627 2.450 nonbonded pdb=" O ASP B 127 " pdb=" HG SER B 130 " model vdw 1.642 2.450 ... (remaining 192092 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'E' } 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: 0.860 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: 0.250 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 33.940 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 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 0.039 7520 Z= 0.180 Angle : 0.565 10.574 10216 Z= 0.242 Chirality : 0.052 0.467 1159 Planarity : 0.003 0.028 1322 Dihedral : 15.299 113.836 3011 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.90 % Allowed : 4.62 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.28), residues: 919 helix: 0.51 (0.51), residues: 126 sheet: 0.95 (0.33), residues: 254 loop : -0.89 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP B 466 HIS 0.002 0.000 HIS B 255 PHE 0.008 0.001 PHE B 414 TYR 0.007 0.001 TYR B 318 ARG 0.002 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 1.147 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: symmetry clash 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: symmetry clash 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: 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 48 GLU cc_start: 0.8725 (tp30) cc_final: 0.8234 (tp30) REVERT: A 49 GLU cc_start: 0.9386 (pt0) cc_final: 0.8927 (pm20) REVERT: A 71 ASP cc_start: 0.8509 (m-30) cc_final: 0.8013 (t0) REVERT: A 420 SER cc_start: 0.9176 (t) cc_final: 0.8892 (p) REVERT: A 435 LEU cc_start: 0.9404 (tp) cc_final: 0.9196 (tp) REVERT: B 131 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8953 (pt) REVERT: B 282 SER cc_start: 0.9329 (m) cc_final: 0.9026 (p) outliers start: 7 outliers final: 3 residues processed: 143 average time/residue: 0.5641 time to fit residues: 101.3418 Evaluate side-chains 90 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 406 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 134 GLN A 333 GLN A 444 GLN ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.064985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.051440 restraints weight = 166902.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.053289 restraints weight = 83659.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.054565 restraints weight = 50242.104| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 7520 Z= 0.328 Angle : 0.691 10.217 10216 Z= 0.341 Chirality : 0.048 0.450 1159 Planarity : 0.005 0.066 1322 Dihedral : 13.603 84.095 1365 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.28 % Allowed : 9.87 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.28), residues: 919 helix: 0.46 (0.49), residues: 123 sheet: 0.51 (0.33), residues: 251 loop : -1.00 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 129 HIS 0.008 0.001 HIS A 112 PHE 0.024 0.002 PHE B 308 TYR 0.019 0.001 TYR B 318 ARG 0.005 0.001 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 94 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 1.180 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8847 (tp30) cc_final: 0.8235 (tp30) REVERT: A 49 GLU cc_start: 0.9462 (pt0) cc_final: 0.8906 (pm20) REVERT: A 71 ASP cc_start: 0.8962 (m-30) cc_final: 0.8181 (t0) REVERT: A 235 TRP cc_start: 0.8898 (t60) cc_final: 0.8354 (t60) REVERT: A 420 SER cc_start: 0.9138 (t) cc_final: 0.8846 (p) REVERT: B 282 SER cc_start: 0.9183 (m) cc_final: 0.8830 (p) outliers start: 10 outliers final: 8 residues processed: 91 average time/residue: 0.5951 time to fit residues: 67.7717 Evaluate side-chains 84 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 61 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.064921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.051147 restraints weight = 164832.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.053018 restraints weight = 82378.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.054338 restraints weight = 49360.630| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7520 Z= 0.175 Angle : 0.575 10.445 10216 Z= 0.275 Chirality : 0.048 0.451 1159 Planarity : 0.004 0.038 1322 Dihedral : 10.770 80.887 1365 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.90 % Allowed : 10.90 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.28), residues: 919 helix: 0.88 (0.51), residues: 123 sheet: 0.54 (0.34), residues: 243 loop : -1.01 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 129 HIS 0.004 0.001 HIS A 112 PHE 0.024 0.001 PHE B 308 TYR 0.012 0.001 TYR A 380 ARG 0.003 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 83 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 1.310 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8892 (tp30) cc_final: 0.8230 (tp30) REVERT: A 49 GLU cc_start: 0.9469 (pt0) cc_final: 0.8929 (pm20) REVERT: A 71 ASP cc_start: 0.8937 (m-30) cc_final: 0.8156 (t0) REVERT: A 168 GLU cc_start: 0.8873 (mp0) cc_final: 0.8390 (mp0) REVERT: A 420 SER cc_start: 0.9003 (t) cc_final: 0.8739 (p) REVERT: B 282 SER cc_start: 0.9206 (m) cc_final: 0.8817 (p) outliers start: 7 outliers final: 6 residues processed: 81 average time/residue: 0.5929 time to fit residues: 61.3650 Evaluate side-chains 80 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 406 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 9 optimal weight: 0.0970 chunk 5 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.061164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.047598 restraints weight = 170658.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.049359 restraints weight = 86555.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.050496 restraints weight = 52320.619| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7520 Z= 0.312 Angle : 0.648 10.211 10216 Z= 0.327 Chirality : 0.046 0.448 1159 Planarity : 0.005 0.063 1322 Dihedral : 8.919 78.381 1365 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 1.67 % Allowed : 10.38 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.27), residues: 919 helix: 0.14 (0.47), residues: 122 sheet: 0.16 (0.34), residues: 238 loop : -1.34 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 129 HIS 0.007 0.001 HIS B 192 PHE 0.039 0.002 PHE B 223 TYR 0.023 0.002 TYR B 318 ARG 0.003 0.001 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 1.122 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: symmetry clash 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: symmetry clash 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: symmetry clash REVERT: A 71 ASP cc_start: 0.8999 (m-30) cc_final: 0.8249 (t0) REVERT: A 168 GLU cc_start: 0.9070 (mp0) cc_final: 0.8653 (mp0) REVERT: A 172 SER cc_start: 0.8654 (t) cc_final: 0.8073 (p) REVERT: A 235 TRP cc_start: 0.9075 (t60) cc_final: 0.8656 (t60) REVERT: B 142 MET cc_start: 0.9324 (mmm) cc_final: 0.8804 (mmm) REVERT: B 266 VAL cc_start: 0.6411 (OUTLIER) cc_final: 0.6026 (p) REVERT: B 282 SER cc_start: 0.9264 (m) cc_final: 0.8886 (p) REVERT: B 295 MET cc_start: 0.8114 (mtt) cc_final: 0.7905 (mtt) REVERT: B 368 LEU cc_start: 0.8863 (tt) cc_final: 0.8468 (mm) outliers start: 13 outliers final: 7 residues processed: 78 average time/residue: 0.5936 time to fit residues: 58.6904 Evaluate side-chains 71 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 266 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 48 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.062064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.048425 restraints weight = 169376.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.050195 restraints weight = 85420.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.051378 restraints weight = 51264.397| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7520 Z= 0.175 Angle : 0.547 10.543 10216 Z= 0.271 Chirality : 0.046 0.455 1159 Planarity : 0.004 0.038 1322 Dihedral : 8.375 75.049 1362 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.28 % Allowed : 11.15 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.28), residues: 919 helix: 0.80 (0.50), residues: 124 sheet: 0.23 (0.34), residues: 233 loop : -1.18 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 129 HIS 0.004 0.001 HIS A 291 PHE 0.026 0.001 PHE B 223 TYR 0.027 0.001 TYR A 329 ARG 0.003 0.000 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 1.253 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.8997 (m-30) cc_final: 0.8255 (t0) REVERT: A 166 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.8422 (m-80) REVERT: A 393 LEU cc_start: 0.9226 (tp) cc_final: 0.9004 (tp) REVERT: B 266 VAL cc_start: 0.6461 (OUTLIER) cc_final: 0.6132 (p) outliers start: 10 outliers final: 7 residues processed: 73 average time/residue: 0.6171 time to fit residues: 56.7088 Evaluate side-chains 70 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 266 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 25 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 82 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 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 = 0.3881 r_free = 0.3881 target = 0.060303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.046689 restraints weight = 178826.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.048402 restraints weight = 89270.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.049541 restraints weight = 53534.654| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7520 Z= 0.282 Angle : 0.608 10.491 10216 Z= 0.306 Chirality : 0.046 0.454 1159 Planarity : 0.004 0.037 1322 Dihedral : 8.296 72.086 1362 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 1.41 % Allowed : 11.79 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.27), residues: 919 helix: 0.50 (0.48), residues: 123 sheet: 0.13 (0.35), residues: 233 loop : -1.32 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 129 HIS 0.006 0.001 HIS B 192 PHE 0.027 0.002 PHE B 223 TYR 0.019 0.002 TYR B 318 ARG 0.008 0.001 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 70 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 1.206 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: symmetry clash 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: symmetry clash 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 71 ASP cc_start: 0.9016 (m-30) cc_final: 0.8283 (t0) REVERT: A 168 GLU cc_start: 0.9074 (mp0) cc_final: 0.8645 (mp0) REVERT: A 393 LEU cc_start: 0.9235 (tp) cc_final: 0.9022 (tp) REVERT: B 142 MET cc_start: 0.9357 (mmm) cc_final: 0.8753 (mmm) REVERT: B 266 VAL cc_start: 0.6901 (OUTLIER) cc_final: 0.6592 (p) outliers start: 11 outliers final: 7 residues processed: 69 average time/residue: 0.6023 time to fit residues: 53.4418 Evaluate side-chains 66 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 266 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 21 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 0.0970 chunk 39 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.060956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.047179 restraints weight = 174250.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.048918 restraints weight = 87472.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.050123 restraints weight = 52467.791| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7520 Z= 0.175 Angle : 0.557 10.679 10216 Z= 0.275 Chirality : 0.046 0.458 1159 Planarity : 0.004 0.038 1322 Dihedral : 8.012 68.231 1362 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.15 % Allowed : 12.44 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.28), residues: 919 helix: 0.92 (0.50), residues: 124 sheet: 0.17 (0.35), residues: 232 loop : -1.20 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 129 HIS 0.005 0.001 HIS A 291 PHE 0.025 0.001 PHE B 223 TYR 0.014 0.001 TYR A 380 ARG 0.002 0.000 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 1.064 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.9060 (m-30) cc_final: 0.8282 (t0) REVERT: B 223 PHE cc_start: 0.7703 (m-80) cc_final: 0.7342 (t80) REVERT: B 266 VAL cc_start: 0.6806 (OUTLIER) cc_final: 0.6489 (p) outliers start: 9 outliers final: 8 residues processed: 68 average time/residue: 0.6034 time to fit residues: 51.9277 Evaluate side-chains 66 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 266 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 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 = 0.3854 r_free = 0.3854 target = 0.058977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.044745 restraints weight = 167291.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.046175 restraints weight = 87581.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.047170 restraints weight = 54382.064| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7520 Z= 0.267 Angle : 0.607 10.596 10216 Z= 0.306 Chirality : 0.045 0.457 1159 Planarity : 0.004 0.051 1322 Dihedral : 7.911 65.149 1362 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.90 % Allowed : 13.21 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.28), residues: 919 helix: 0.73 (0.48), residues: 124 sheet: 0.12 (0.35), residues: 232 loop : -1.32 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 129 HIS 0.006 0.001 HIS B 192 PHE 0.020 0.002 PHE B 308 TYR 0.020 0.002 TYR B 318 ARG 0.003 0.001 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 1.369 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: symmetry clash 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: symmetry clash 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 71 ASP cc_start: 0.9023 (m-30) cc_final: 0.8241 (t0) REVERT: A 168 GLU cc_start: 0.9073 (mp0) cc_final: 0.8657 (mp0) REVERT: B 22 MET cc_start: 0.9655 (mmm) cc_final: 0.9360 (ppp) REVERT: B 142 MET cc_start: 0.9367 (mmm) cc_final: 0.8786 (mmm) REVERT: B 223 PHE cc_start: 0.7869 (m-80) cc_final: 0.7520 (t80) outliers start: 7 outliers final: 7 residues processed: 65 average time/residue: 0.6346 time to fit residues: 52.5834 Evaluate side-chains 64 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 138 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 53 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.060374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.046800 restraints weight = 170790.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.048505 restraints weight = 85615.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.049630 restraints weight = 51375.471| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7520 Z= 0.157 Angle : 0.547 10.744 10216 Z= 0.269 Chirality : 0.046 0.458 1159 Planarity : 0.004 0.037 1322 Dihedral : 7.596 62.282 1361 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.90 % Allowed : 13.33 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.28), residues: 919 helix: 1.25 (0.51), residues: 124 sheet: 0.25 (0.35), residues: 235 loop : -1.17 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 260 HIS 0.005 0.001 HIS A 291 PHE 0.019 0.001 PHE B 308 TYR 0.013 0.001 TYR A 380 ARG 0.002 0.000 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 1.176 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: symmetry clash 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: symmetry clash 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 71 ASP cc_start: 0.9042 (m-30) cc_final: 0.8279 (t0) REVERT: B 22 MET cc_start: 0.9645 (mmm) cc_final: 0.9369 (ppp) REVERT: B 223 PHE cc_start: 0.7689 (m-80) cc_final: 0.7454 (t80) outliers start: 7 outliers final: 7 residues processed: 69 average time/residue: 0.5889 time to fit residues: 51.5096 Evaluate side-chains 66 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 72 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 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 = 0.3858 r_free = 0.3858 target = 0.058820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.044789 restraints weight = 166738.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.046223 restraints weight = 85888.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.047447 restraints weight = 52953.173| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.5558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7520 Z= 0.243 Angle : 0.592 10.717 10216 Z= 0.296 Chirality : 0.045 0.457 1159 Planarity : 0.004 0.036 1322 Dihedral : 7.557 60.860 1361 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.90 % Allowed : 13.59 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.28), residues: 919 helix: 0.85 (0.49), residues: 123 sheet: 0.22 (0.36), residues: 233 loop : -1.27 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 129 HIS 0.005 0.001 HIS B 192 PHE 0.018 0.002 PHE B 308 TYR 0.019 0.001 TYR B 318 ARG 0.003 0.001 ARG A 449 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 1.434 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: symmetry clash 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: 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 71 ASP cc_start: 0.9047 (m-30) cc_final: 0.8250 (t0) REVERT: A 168 GLU cc_start: 0.9059 (mp0) cc_final: 0.8638 (mp0) REVERT: B 22 MET cc_start: 0.9646 (mmm) cc_final: 0.9353 (ppp) outliers start: 7 outliers final: 6 residues processed: 67 average time/residue: 0.6177 time to fit residues: 52.7310 Evaluate side-chains 63 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 58 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 67 optimal weight: 0.0050 chunk 28 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 79 optimal weight: 0.3980 chunk 53 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.060237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.046599 restraints weight = 171043.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.048304 restraints weight = 84858.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.049439 restraints weight = 50705.944| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.5541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7520 Z= 0.155 Angle : 0.564 10.814 10216 Z= 0.277 Chirality : 0.047 0.458 1159 Planarity : 0.004 0.037 1322 Dihedral : 7.332 58.811 1359 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.90 % Allowed : 13.72 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.28), residues: 919 helix: 1.07 (0.51), residues: 123 sheet: 0.29 (0.35), residues: 233 loop : -1.15 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 260 HIS 0.006 0.001 HIS A 291 PHE 0.043 0.001 PHE B 223 TYR 0.013 0.001 TYR A 380 ARG 0.005 0.000 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4951.71 seconds wall clock time: 88 minutes 36.07 seconds (5316.07 seconds total)