Starting phenix.real_space_refine on Thu Sep 18 06:00:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9der_46794/09_2025/9der_46794_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9der_46794/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9der_46794/09_2025/9der_46794_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9der_46794/09_2025/9der_46794_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9der_46794/09_2025/9der_46794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9der_46794/09_2025/9der_46794.map" } resolution = 3.9 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= 0.014 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.24, per 1000 atoms: 0.23 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: 1.52 Conformation dependent library (CDL) restraints added in 466.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.42 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: 3.98 Time building geometry restraints manager: 2.03 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.030 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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: 20.140 ------------------------------------------------------------------------------- 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 7551 Z= 0.135 Angle : 0.589 10.574 10294 Z= 0.248 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG B 214 TYR 0.007 0.001 TYR B 318 PHE 0.008 0.001 PHE B 414 TRP 0.006 0.000 TRP B 466 HIS 0.002 0.000 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7520) covalent geometry : angle 0.56467 (10216) SS BOND : bond 0.00128 ( 15) SS BOND : angle 0.50332 ( 30) hydrogen bonds : bond 0.17080 ( 253) hydrogen bonds : angle 7.43104 ( 660) link_BETA1-4 : bond 0.00682 ( 10) link_BETA1-4 : angle 2.46635 ( 30) link_BETA1-6 : bond 0.00396 ( 1) link_BETA1-6 : angle 1.29029 ( 3) link_NAG-ASN : bond 0.00611 ( 5) link_NAG-ASN : angle 2.82170 ( 15) *********************** 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 : 0.424 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: 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: 0.8954 (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: 0.2858 time to fit residues: 51.1401 Evaluate side-chains 88 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.0470 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 overall best weight: 1.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 333 GLN A 372 ASN A 444 GLN B 280 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.067156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.053054 restraints weight = 160560.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.055078 restraints weight = 79985.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.056604 restraints weight = 47824.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.057573 restraints weight = 31877.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.058293 restraints weight = 23227.019| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7551 Z= 0.153 Angle : 0.633 10.433 10294 Z= 0.300 Chirality : 0.047 0.452 1159 Planarity : 0.004 0.059 1322 Dihedral : 14.293 85.823 1365 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.28 % Allowed : 9.62 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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 aren not related in a simple way. whole: -0.24 (0.28), residues: 919 helix: 0.90 (0.51), residues: 123 sheet: 0.64 (0.32), residues: 261 loop : -0.84 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 320 TYR 0.013 0.001 TYR B 318 PHE 0.023 0.001 PHE B 308 TRP 0.007 0.001 TRP B 466 HIS 0.004 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 7520) covalent geometry : angle 0.60703 (10216) SS BOND : bond 0.00430 ( 15) SS BOND : angle 0.95440 ( 30) hydrogen bonds : bond 0.04423 ( 253) hydrogen bonds : angle 6.12402 ( 660) link_BETA1-4 : bond 0.00748 ( 10) link_BETA1-4 : angle 2.57783 ( 30) link_BETA1-6 : bond 0.00713 ( 1) link_BETA1-6 : angle 3.57622 ( 3) link_NAG-ASN : bond 0.00535 ( 5) link_NAG-ASN : angle 2.56642 ( 15) *********************** 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 : 0.414 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: 0.8683 (tp30) cc_final: 0.8182 (tp30) REVERT: A 49 GLU cc_start: 0.9415 (pt0) cc_final: 0.8819 (pm20) REVERT: A 71 ASP cc_start: 0.8802 (m-30) cc_final: 0.8069 (t0) REVERT: A 127 VAL cc_start: 0.8362 (m) cc_final: 0.7735 (t) REVERT: A 420 SER cc_start: 0.9174 (t) cc_final: 0.8908 (p) REVERT: B 131 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8935 (pt) REVERT: B 282 SER cc_start: 0.9259 (m) cc_final: 0.8913 (p) outliers start: 10 outliers final: 7 residues processed: 91 average time/residue: 0.2875 time to fit residues: 32.7291 Evaluate side-chains 83 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU 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 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 54 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN B 82 GLN ** B 133 ASN ** 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 = 0.3980 r_free = 0.3980 target = 0.064167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.050660 restraints weight = 168345.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.052510 restraints weight = 83876.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.053778 restraints weight = 49967.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.054606 restraints weight = 33387.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.055154 restraints weight = 24478.685| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 7551 Z= 0.189 Angle : 0.655 10.293 10294 Z= 0.311 Chirality : 0.048 0.450 1159 Planarity : 0.004 0.048 1322 Dihedral : 10.317 81.175 1365 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.54 % Allowed : 10.38 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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 aren not related in a simple way. whole: -0.58 (0.28), residues: 919 helix: 0.52 (0.49), residues: 122 sheet: 0.55 (0.34), residues: 247 loop : -1.07 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 449 TYR 0.017 0.001 TYR B 318 PHE 0.022 0.002 PHE B 223 TRP 0.010 0.001 TRP B 129 HIS 0.006 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 7520) covalent geometry : angle 0.63021 (10216) SS BOND : bond 0.00188 ( 15) SS BOND : angle 0.82700 ( 30) hydrogen bonds : bond 0.03881 ( 253) hydrogen bonds : angle 5.78560 ( 660) link_BETA1-4 : bond 0.00587 ( 10) link_BETA1-4 : angle 2.73018 ( 30) link_BETA1-6 : bond 0.00417 ( 1) link_BETA1-6 : angle 3.09808 ( 3) link_NAG-ASN : bond 0.00365 ( 5) link_NAG-ASN : angle 2.47858 ( 15) *********************** 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 84 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.392 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 48 GLU cc_start: 0.8843 (tp30) cc_final: 0.8214 (tp30) REVERT: A 49 GLU cc_start: 0.9438 (pt0) cc_final: 0.8896 (pm20) REVERT: A 71 ASP cc_start: 0.8896 (m-30) cc_final: 0.8157 (t0) REVERT: A 168 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8659 (mp0) REVERT: A 235 TRP cc_start: 0.8846 (t60) cc_final: 0.8365 (t60) REVERT: B 282 SER cc_start: 0.9210 (m) cc_final: 0.8866 (p) REVERT: B 295 MET cc_start: 0.8424 (mtt) cc_final: 0.8146 (mtt) outliers start: 12 outliers final: 9 residues processed: 78 average time/residue: 0.2869 time to fit residues: 27.9105 Evaluate side-chains 79 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 168 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 118 MET 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 13 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.063309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.049622 restraints weight = 168225.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.051428 restraints weight = 84052.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.052697 restraints weight = 50455.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.053559 restraints weight = 33882.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.054115 restraints weight = 24968.621| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7551 Z= 0.149 Angle : 0.577 10.327 10294 Z= 0.278 Chirality : 0.046 0.451 1159 Planarity : 0.004 0.048 1322 Dihedral : 8.752 77.178 1365 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.67 % Allowed : 10.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.28), residues: 919 helix: 0.90 (0.51), residues: 122 sheet: 0.53 (0.35), residues: 231 loop : -1.09 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 320 TYR 0.014 0.001 TYR B 318 PHE 0.039 0.002 PHE B 223 TRP 0.009 0.001 TRP B 129 HIS 0.005 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 7520) covalent geometry : angle 0.55308 (10216) SS BOND : bond 0.00133 ( 15) SS BOND : angle 0.60634 ( 30) hydrogen bonds : bond 0.03402 ( 253) hydrogen bonds : angle 5.58087 ( 660) link_BETA1-4 : bond 0.00650 ( 10) link_BETA1-4 : angle 2.55920 ( 30) link_BETA1-6 : bond 0.00601 ( 1) link_BETA1-6 : angle 1.78327 ( 3) link_NAG-ASN : bond 0.00417 ( 5) link_NAG-ASN : angle 2.41991 ( 15) *********************** 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 83 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.430 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: A 49 GLU cc_start: 0.9442 (pt0) cc_final: 0.9166 (pm20) REVERT: A 71 ASP cc_start: 0.8927 (m-30) cc_final: 0.8204 (t0) REVERT: A 194 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8571 (tt) REVERT: A 235 TRP cc_start: 0.8912 (t60) cc_final: 0.8452 (t60) REVERT: B 266 VAL cc_start: 0.5916 (OUTLIER) cc_final: 0.5510 (p) REVERT: B 282 SER cc_start: 0.9177 (m) cc_final: 0.8786 (p) outliers start: 13 outliers final: 8 residues processed: 77 average time/residue: 0.2917 time to fit residues: 28.4504 Evaluate side-chains 78 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 194 LEU 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 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 61 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.061020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.047423 restraints weight = 173219.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.049189 restraints weight = 86525.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.050351 restraints weight = 51875.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.051176 restraints weight = 35151.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.051725 restraints weight = 25946.911| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7551 Z= 0.197 Angle : 0.623 10.390 10294 Z= 0.305 Chirality : 0.045 0.452 1159 Planarity : 0.004 0.033 1322 Dihedral : 8.275 72.731 1364 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.67 % Allowed : 10.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.27), residues: 919 helix: 0.59 (0.48), residues: 124 sheet: 0.26 (0.35), residues: 235 loop : -1.25 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 335 TYR 0.019 0.002 TYR B 318 PHE 0.032 0.002 PHE B 223 TRP 0.010 0.001 TRP B 129 HIS 0.006 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 7520) covalent geometry : angle 0.60365 (10216) SS BOND : bond 0.00159 ( 15) SS BOND : angle 0.62598 ( 30) hydrogen bonds : bond 0.03461 ( 253) hydrogen bonds : angle 5.63184 ( 660) link_BETA1-4 : bond 0.00548 ( 10) link_BETA1-4 : angle 2.39217 ( 30) link_BETA1-6 : bond 0.00190 ( 1) link_BETA1-6 : angle 1.39330 ( 3) link_NAG-ASN : bond 0.00371 ( 5) link_NAG-ASN : angle 2.42783 ( 15) *********************** 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 78 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.423 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 49 GLU cc_start: 0.9425 (pt0) cc_final: 0.9150 (pm20) REVERT: A 71 ASP cc_start: 0.8951 (m-30) cc_final: 0.8223 (t0) REVERT: A 172 SER cc_start: 0.8569 (t) cc_final: 0.8020 (p) REVERT: A 235 TRP cc_start: 0.9038 (t60) cc_final: 0.8602 (t60) REVERT: B 142 MET cc_start: 0.9305 (mmm) cc_final: 0.8771 (mmm) REVERT: B 266 VAL cc_start: 0.6484 (OUTLIER) cc_final: 0.6182 (p) outliers start: 13 outliers final: 9 residues processed: 73 average time/residue: 0.2905 time to fit residues: 27.0335 Evaluate side-chains 72 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 194 LEU 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 83 VAL 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 81 optimal weight: 0.0270 chunk 90 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 75 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 overall best weight: 1.2442 ------------------------------------------------------------------------------- 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 = 0.3919 r_free = 0.3919 target = 0.061789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.048096 restraints weight = 167870.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.049841 restraints weight = 84561.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.051020 restraints weight = 50843.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.051882 restraints weight = 34503.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.052406 restraints weight = 25418.878| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7551 Z= 0.116 Angle : 0.568 10.638 10294 Z= 0.273 Chirality : 0.046 0.456 1159 Planarity : 0.004 0.034 1322 Dihedral : 7.909 68.653 1362 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.28 % Allowed : 12.05 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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 aren not related in a simple way. whole: -0.68 (0.28), residues: 919 helix: 0.99 (0.51), residues: 124 sheet: 0.29 (0.35), residues: 233 loop : -1.15 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 335 TYR 0.027 0.001 TYR A 329 PHE 0.023 0.001 PHE B 223 TRP 0.008 0.001 TRP B 129 HIS 0.003 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 7520) covalent geometry : angle 0.54741 (10216) SS BOND : bond 0.00121 ( 15) SS BOND : angle 0.51032 ( 30) hydrogen bonds : bond 0.03037 ( 253) hydrogen bonds : angle 5.46582 ( 660) link_BETA1-4 : bond 0.00642 ( 10) link_BETA1-4 : angle 2.30104 ( 30) link_BETA1-6 : bond 0.00403 ( 1) link_BETA1-6 : angle 1.36246 ( 3) link_NAG-ASN : bond 0.00405 ( 5) link_NAG-ASN : angle 2.33964 ( 15) *********************** 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 77 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.413 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 49 GLU cc_start: 0.9443 (pt0) cc_final: 0.9172 (pm20) REVERT: A 71 ASP cc_start: 0.9041 (m-30) cc_final: 0.8277 (t0) REVERT: A 393 LEU cc_start: 0.9243 (tp) cc_final: 0.9015 (tp) REVERT: B 223 PHE cc_start: 0.7593 (m-80) cc_final: 0.7250 (t80) REVERT: B 266 VAL cc_start: 0.6377 (OUTLIER) cc_final: 0.6057 (p) outliers start: 10 outliers final: 7 residues processed: 74 average time/residue: 0.2777 time to fit residues: 26.1966 Evaluate side-chains 72 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU 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 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 10 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 73 optimal weight: 0.2980 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.3901 r_free = 0.3901 target = 0.061050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.047612 restraints weight = 171787.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.049300 restraints weight = 85391.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.050453 restraints weight = 51163.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.051289 restraints weight = 34673.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.051853 restraints weight = 25486.026| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7551 Z= 0.137 Angle : 0.579 10.596 10294 Z= 0.278 Chirality : 0.046 0.456 1159 Planarity : 0.004 0.032 1322 Dihedral : 7.721 65.123 1362 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.54 % Allowed : 11.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.28), residues: 919 helix: 1.06 (0.51), residues: 124 sheet: 0.35 (0.35), residues: 233 loop : -1.19 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 335 TYR 0.014 0.001 TYR A 329 PHE 0.019 0.001 PHE B 223 TRP 0.009 0.001 TRP A 235 HIS 0.004 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7520) covalent geometry : angle 0.55750 (10216) SS BOND : bond 0.00250 ( 15) SS BOND : angle 0.97441 ( 30) hydrogen bonds : bond 0.03029 ( 253) hydrogen bonds : angle 5.43508 ( 660) link_BETA1-4 : bond 0.00592 ( 10) link_BETA1-4 : angle 2.27873 ( 30) link_BETA1-6 : bond 0.00356 ( 1) link_BETA1-6 : angle 1.41772 ( 3) link_NAG-ASN : bond 0.00371 ( 5) link_NAG-ASN : angle 2.46291 ( 15) *********************** 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 74 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.407 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: A 49 GLU cc_start: 0.9438 (pt0) cc_final: 0.9208 (pm20) REVERT: A 71 ASP cc_start: 0.9000 (m-30) cc_final: 0.8228 (t0) REVERT: A 393 LEU cc_start: 0.9249 (tp) cc_final: 0.9047 (tp) REVERT: B 142 MET cc_start: 0.9323 (mmm) cc_final: 0.8756 (mmm) REVERT: B 266 VAL cc_start: 0.6614 (OUTLIER) cc_final: 0.6308 (p) outliers start: 12 outliers final: 11 residues processed: 71 average time/residue: 0.2923 time to fit residues: 26.2265 Evaluate side-chains 74 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU 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 127 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 Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 406 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 87 optimal weight: 30.0000 chunk 10 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.059162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.045087 restraints weight = 166084.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.046592 restraints weight = 87592.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.047600 restraints weight = 53825.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.048347 restraints weight = 37482.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.048847 restraints weight = 28210.974| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7551 Z= 0.183 Angle : 0.615 10.581 10294 Z= 0.303 Chirality : 0.045 0.458 1159 Planarity : 0.004 0.030 1322 Dihedral : 7.650 62.795 1362 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 2.05 % Allowed : 11.67 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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 aren not related in a simple way. whole: -0.89 (0.28), residues: 919 helix: 0.74 (0.48), residues: 124 sheet: 0.19 (0.36), residues: 232 loop : -1.29 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 150 TYR 0.017 0.002 TYR B 318 PHE 0.025 0.002 PHE B 223 TRP 0.010 0.002 TRP B 129 HIS 0.006 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 7520) covalent geometry : angle 0.58837 (10216) SS BOND : bond 0.00139 ( 15) SS BOND : angle 1.91103 ( 30) hydrogen bonds : bond 0.03401 ( 253) hydrogen bonds : angle 5.58314 ( 660) link_BETA1-4 : bond 0.00641 ( 10) link_BETA1-4 : angle 2.33869 ( 30) link_BETA1-6 : bond 0.00317 ( 1) link_BETA1-6 : angle 1.35669 ( 3) link_NAG-ASN : bond 0.00358 ( 5) link_NAG-ASN : angle 2.34535 ( 15) *********************** 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 76 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.474 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 49 GLU cc_start: 0.9416 (pt0) cc_final: 0.9170 (pm20) REVERT: A 71 ASP cc_start: 0.8989 (m-30) cc_final: 0.8193 (t0) REVERT: B 142 MET cc_start: 0.9321 (mmm) cc_final: 0.8629 (mmm) REVERT: B 266 VAL cc_start: 0.6820 (OUTLIER) cc_final: 0.6520 (p) outliers start: 16 outliers final: 13 residues processed: 73 average time/residue: 0.2727 time to fit residues: 25.3855 Evaluate side-chains 73 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU 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 288 TYR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 127 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 Chi-restraints excluded: chain B residue 406 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 74 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 87 optimal weight: 30.0000 chunk 40 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.1980 chunk 64 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.059940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.046143 restraints weight = 171767.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.047861 restraints weight = 86119.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.048978 restraints weight = 51815.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.049779 restraints weight = 35393.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.050343 restraints weight = 26210.146| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.5295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7551 Z= 0.121 Angle : 0.580 10.757 10294 Z= 0.281 Chirality : 0.046 0.458 1159 Planarity : 0.004 0.032 1322 Dihedral : 7.465 60.407 1362 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.28 % Allowed : 12.44 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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 aren not related in a simple way. whole: -0.70 (0.28), residues: 919 helix: 1.11 (0.50), residues: 124 sheet: 0.31 (0.36), residues: 233 loop : -1.22 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 461 TYR 0.013 0.001 TYR A 380 PHE 0.018 0.001 PHE B 223 TRP 0.014 0.001 TRP B 466 HIS 0.003 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7520) covalent geometry : angle 0.55858 (10216) SS BOND : bond 0.00319 ( 15) SS BOND : angle 1.06640 ( 30) hydrogen bonds : bond 0.03095 ( 253) hydrogen bonds : angle 5.44766 ( 660) link_BETA1-4 : bond 0.00587 ( 10) link_BETA1-4 : angle 2.25978 ( 30) link_BETA1-6 : bond 0.00381 ( 1) link_BETA1-6 : angle 1.27965 ( 3) link_NAG-ASN : bond 0.00411 ( 5) link_NAG-ASN : angle 2.29667 ( 15) *********************** 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 72 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.359 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 49 GLU cc_start: 0.9386 (pt0) cc_final: 0.9162 (pm20) REVERT: A 71 ASP cc_start: 0.8985 (m-30) cc_final: 0.8216 (t0) REVERT: B 66 ASP cc_start: 0.9078 (p0) cc_final: 0.8548 (p0) REVERT: B 142 MET cc_start: 0.9325 (mmm) cc_final: 0.8703 (mmm) REVERT: B 368 LEU cc_start: 0.8795 (tt) cc_final: 0.8423 (mm) outliers start: 10 outliers final: 9 residues processed: 70 average time/residue: 0.2673 time to fit residues: 23.8253 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 : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU 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 127 ASP Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 406 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 53 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 85 optimal weight: 0.0770 chunk 29 optimal weight: 1.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- 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 = 0.3886 r_free = 0.3886 target = 0.060198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.046526 restraints weight = 173118.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.048282 restraints weight = 85768.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.049420 restraints weight = 50989.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.050255 restraints weight = 34508.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.050826 restraints weight = 25362.040| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7551 Z= 0.109 Angle : 0.570 10.768 10294 Z= 0.276 Chirality : 0.046 0.457 1159 Planarity : 0.004 0.032 1322 Dihedral : 7.284 58.312 1359 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.15 % Allowed : 12.82 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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 aren not related in a simple way. whole: -0.65 (0.28), residues: 919 helix: 1.14 (0.51), residues: 124 sheet: 0.35 (0.35), residues: 233 loop : -1.19 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 202 TYR 0.012 0.001 TYR A 380 PHE 0.017 0.001 PHE B 308 TRP 0.009 0.001 TRP B 466 HIS 0.002 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 7520) covalent geometry : angle 0.54987 (10216) SS BOND : bond 0.00288 ( 15) SS BOND : angle 0.91634 ( 30) hydrogen bonds : bond 0.03061 ( 253) hydrogen bonds : angle 5.40031 ( 660) link_BETA1-4 : bond 0.00634 ( 10) link_BETA1-4 : angle 2.24769 ( 30) link_BETA1-6 : bond 0.00450 ( 1) link_BETA1-6 : angle 1.32338 ( 3) link_NAG-ASN : bond 0.00435 ( 5) link_NAG-ASN : angle 2.28278 ( 15) ********************** 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 70 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.377 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: 0.9003 (m-30) cc_final: 0.8229 (t0) REVERT: B 66 ASP cc_start: 0.9000 (p0) cc_final: 0.8478 (p0) REVERT: B 142 MET cc_start: 0.9342 (mmm) cc_final: 0.8709 (mmm) REVERT: B 368 LEU cc_start: 0.8793 (tt) cc_final: 0.8439 (mm) outliers start: 9 outliers final: 8 residues processed: 67 average time/residue: 0.2826 time to fit residues: 24.0063 Evaluate side-chains 67 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU 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 138 LEU Chi-restraints excluded: chain B residue 406 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 52 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.058521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.044287 restraints weight = 167110.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.045816 restraints weight = 86415.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.046850 restraints weight = 54168.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.047641 restraints weight = 37681.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.048143 restraints weight = 28328.124| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.5707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7551 Z= 0.176 Angle : 0.611 10.734 10294 Z= 0.302 Chirality : 0.045 0.458 1159 Planarity : 0.004 0.051 1322 Dihedral : 7.329 59.551 1359 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 1.28 % Allowed : 13.08 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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 aren not related in a simple way. whole: -0.82 (0.28), residues: 919 helix: 0.96 (0.49), residues: 117 sheet: 0.20 (0.35), residues: 240 loop : -1.26 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 90 TYR 0.019 0.001 TYR B 318 PHE 0.015 0.002 PHE B 308 TRP 0.010 0.002 TRP A 235 HIS 0.006 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 7520) covalent geometry : angle 0.59237 (10216) SS BOND : bond 0.00223 ( 15) SS BOND : angle 0.93355 ( 30) hydrogen bonds : bond 0.03353 ( 253) hydrogen bonds : angle 5.62755 ( 660) link_BETA1-4 : bond 0.00554 ( 10) link_BETA1-4 : angle 2.19717 ( 30) link_BETA1-6 : bond 0.00352 ( 1) link_BETA1-6 : angle 1.43829 ( 3) link_NAG-ASN : bond 0.00358 ( 5) link_NAG-ASN : angle 2.32488 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2984.28 seconds wall clock time: 51 minutes 34.55 seconds (3094.55 seconds total)