Starting phenix.real_space_refine on Fri Jun 13 01:29:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9der_46794/06_2025/9der_46794_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9der_46794/06_2025/9der_46794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9der_46794/06_2025/9der_46794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9der_46794/06_2025/9der_46794.map" model { file = "/net/cci-nas-00/data/ceres_data/9der_46794/06_2025/9der_46794_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9der_46794/06_2025/9der_46794_trim.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 6 9.91 5 Mg 1 5.21 5 S 44 5.16 5 C 4612 2.51 5 N 1232 2.21 5 O 1469 1.98 5 H 6843 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14207 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 6697 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 26, 'TRANS': 421} Chain: "B" Number of atoms: 7265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 7265 Classifications: {'peptide': 477} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 24, 'TRANS': 449} Chain breaks: 1 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 35 Unusual residues: {' CA': 2, ' MG': 1} Classifications: {'peptide': 1, 'undetermined': 3, 'water': 2} Link IDs: {None: 5} Time building chain proxies: 7.53, per 1000 atoms: 0.53 Number of scatterers: 14207 At special positions: 0 Unit cell: (82.08, 101.52, 166.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 6 19.99 S 44 16.00 Mg 1 11.99 O 1469 8.00 N 1232 7.00 C 4612 6.00 H 6843 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 167 " distance=2.03 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 23 " distance=2.03 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 435 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 38 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 406 " - pdb=" SG CYS B 433 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 448 " - pdb=" SG CYS B 460 " distance=2.03 Simple disulfide: pdb=" SG CYS B 460 " - pdb=" SG CYS B 471 " distance=2.03 Simple disulfide: pdb=" SG CYS B 462 " - pdb=" SG CYS B 471 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " BMA E 3 " - " BMA E 4 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " BETA1-6 " BMA D 3 " - " BMA D 4 " NAG-ASN " NAG C 1 " - " ASN A 249 " " NAG D 1 " - " ASN B 320 " " NAG E 1 " - " ASN A 15 " " NAG F 1 " - " ASN B 371 " " NAG G 1 " - " ASN B 99 " Time building additional restraints: 4.19 Conformation dependent library (CDL) restraints added in 1.2 seconds 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1686 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 13 sheets defined 17.2% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 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: 4.71 Time building geometry restraints manager: 4.96 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: 34.540 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: 0.270 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 33.370 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.110 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.28), residues: 919 helix: 0.51 (0.51), residues: 126 sheet: 0.95 (0.33), residues: 254 loop : -0.89 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP B 466 HIS 0.002 0.000 HIS B 255 PHE 0.008 0.001 PHE B 414 TYR 0.007 0.001 TYR B 318 ARG 0.002 0.000 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00611 ( 5) link_NAG-ASN : angle 2.82170 ( 15) link_BETA1-4 : bond 0.00682 ( 10) link_BETA1-4 : angle 2.46635 ( 30) hydrogen bonds : bond 0.17080 ( 253) hydrogen bonds : angle 7.43104 ( 660) link_BETA1-6 : bond 0.00396 ( 1) link_BETA1-6 : angle 1.29029 ( 3) SS BOND : bond 0.00128 ( 15) SS BOND : angle 0.50332 ( 30) covalent geometry : bond 0.00278 ( 7520) covalent geometry : angle 0.56467 (10216) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8725 (tp30) cc_final: 0.8234 (tp30) REVERT: A 49 GLU cc_start: 0.9386 (pt0) cc_final: 0.8927 (pm20) REVERT: A 71 ASP cc_start: 0.8509 (m-30) cc_final: 0.8013 (t0) REVERT: A 420 SER cc_start: 0.9176 (t) cc_final: 0.8892 (p) REVERT: A 435 LEU cc_start: 0.9404 (tp) cc_final: 0.9196 (tp) REVERT: B 131 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8953 (pt) REVERT: B 282 SER cc_start: 0.9329 (m) cc_final: 0.9026 (p) outliers start: 7 outliers final: 3 residues processed: 143 average time/residue: 0.5361 time to fit residues: 96.3942 Evaluate side-chains 90 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 406 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 134 GLN A 444 GLN B 86 GLN ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.062933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.049506 restraints weight = 172524.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.051277 restraints weight = 86924.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.052510 restraints weight = 52295.718| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 7551 Z= 0.329 Angle : 0.849 10.072 10294 Z= 0.416 Chirality : 0.051 0.447 1159 Planarity : 0.006 0.093 1322 Dihedral : 12.601 79.682 1365 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.67 % Allowed : 9.49 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.27), residues: 919 helix: -0.14 (0.46), residues: 123 sheet: 0.32 (0.34), residues: 248 loop : -1.23 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 129 HIS 0.010 0.002 HIS A 112 PHE 0.032 0.002 PHE B 308 TYR 0.025 0.002 TYR B 318 ARG 0.008 0.001 ARG A 320 Details of bonding type rmsd link_NAG-ASN : bond 0.00485 ( 5) link_NAG-ASN : angle 2.69770 ( 15) link_BETA1-4 : bond 0.00695 ( 10) link_BETA1-4 : angle 3.16918 ( 30) hydrogen bonds : bond 0.04802 ( 253) hydrogen bonds : angle 6.41459 ( 660) link_BETA1-6 : bond 0.00500 ( 1) link_BETA1-6 : angle 4.97499 ( 3) SS BOND : bond 0.01448 ( 15) SS BOND : angle 1.56106 ( 30) covalent geometry : bond 0.00657 ( 7520) covalent geometry : angle 0.82005 (10216) *********************** 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 89 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8938 (tp30) cc_final: 0.8306 (tp30) REVERT: A 49 GLU cc_start: 0.9444 (pt0) cc_final: 0.8879 (pm20) REVERT: A 71 ASP cc_start: 0.9015 (m-30) cc_final: 0.8252 (t0) REVERT: A 235 TRP cc_start: 0.9026 (t60) cc_final: 0.8489 (t60) REVERT: B 266 VAL cc_start: 0.5636 (OUTLIER) cc_final: 0.5190 (p) REVERT: B 282 SER cc_start: 0.9256 (m) cc_final: 0.8904 (p) outliers start: 13 outliers final: 9 residues processed: 86 average time/residue: 0.6130 time to fit residues: 66.2056 Evaluate side-chains 80 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 61 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 0.0980 chunk 29 optimal weight: 2.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** 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 = 0.3933 r_free = 0.3933 target = 0.062533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.048875 restraints weight = 169026.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.050636 restraints weight = 83337.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.051901 restraints weight = 49874.592| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3618 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= 0.182 Angle : 0.637 10.349 10294 Z= 0.307 Chirality : 0.047 0.451 1159 Planarity : 0.004 0.037 1322 Dihedral : 10.459 80.268 1365 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.41 % Allowed : 9.74 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.27), residues: 919 helix: 0.38 (0.48), residues: 123 sheet: 0.37 (0.35), residues: 231 loop : -1.20 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 129 HIS 0.006 0.001 HIS A 112 PHE 0.027 0.002 PHE B 223 TYR 0.014 0.001 TYR A 380 ARG 0.003 0.000 ARG A 279 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 5) link_NAG-ASN : angle 2.53362 ( 15) link_BETA1-4 : bond 0.00598 ( 10) link_BETA1-4 : angle 2.73943 ( 30) hydrogen bonds : bond 0.04031 ( 253) hydrogen bonds : angle 5.98404 ( 660) link_BETA1-6 : bond 0.00565 ( 1) link_BETA1-6 : angle 3.58483 ( 3) SS BOND : bond 0.00276 ( 15) SS BOND : angle 0.83686 ( 30) covalent geometry : bond 0.00362 ( 7520) covalent geometry : angle 0.60933 (10216) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 83 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 1.202 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: 0.9452 (pt0) cc_final: 0.9167 (pm20) REVERT: A 71 ASP cc_start: 0.9001 (m-30) cc_final: 0.8234 (t0) REVERT: A 235 TRP cc_start: 0.8958 (t60) cc_final: 0.8486 (t60) REVERT: A 393 LEU cc_start: 0.9184 (tp) cc_final: 0.8970 (tp) REVERT: B 142 MET cc_start: 0.9341 (mmm) cc_final: 0.8624 (mmm) REVERT: B 266 VAL cc_start: 0.6051 (OUTLIER) cc_final: 0.5731 (p) REVERT: B 282 SER cc_start: 0.9241 (m) cc_final: 0.8869 (p) outliers start: 11 outliers final: 8 residues processed: 79 average time/residue: 0.5679 time to fit residues: 57.1491 Evaluate side-chains 75 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 1.226 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 406 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 17 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 65 optimal weight: 0.0670 chunk 77 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.062633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.048916 restraints weight = 169119.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.050743 restraints weight = 84076.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.051923 restraints weight = 50122.596| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3878 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= 0.134 Angle : 0.587 10.474 10294 Z= 0.281 Chirality : 0.046 0.453 1159 Planarity : 0.004 0.037 1322 Dihedral : 9.169 77.997 1365 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.03 % Allowed : 10.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.28), residues: 919 helix: 0.84 (0.51), residues: 123 sheet: 0.31 (0.35), residues: 231 loop : -1.15 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 129 HIS 0.004 0.001 HIS A 112 PHE 0.021 0.001 PHE B 223 TYR 0.024 0.001 TYR A 329 ARG 0.003 0.000 ARG A 335 Details of bonding type rmsd link_NAG-ASN : bond 0.00409 ( 5) link_NAG-ASN : angle 2.42422 ( 15) link_BETA1-4 : bond 0.00634 ( 10) link_BETA1-4 : angle 2.60825 ( 30) hydrogen bonds : bond 0.03351 ( 253) hydrogen bonds : angle 5.75803 ( 660) link_BETA1-6 : bond 0.00539 ( 1) link_BETA1-6 : angle 2.40822 ( 3) SS BOND : bond 0.00108 ( 15) SS BOND : angle 0.59169 ( 30) covalent geometry : bond 0.00284 ( 7520) covalent geometry : angle 0.56167 (10216) *********************** 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 74 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 1.072 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: 0.9429 (pt0) cc_final: 0.9142 (pm20) REVERT: A 71 ASP cc_start: 0.8981 (m-30) cc_final: 0.8248 (t0) REVERT: A 172 SER cc_start: 0.8546 (t) cc_final: 0.7957 (p) REVERT: A 235 TRP cc_start: 0.8980 (t60) cc_final: 0.8501 (t60) REVERT: A 393 LEU cc_start: 0.9182 (tp) cc_final: 0.8979 (tp) REVERT: B 266 VAL cc_start: 0.6255 (OUTLIER) cc_final: 0.5930 (p) REVERT: B 282 SER cc_start: 0.9239 (m) cc_final: 0.8859 (p) outliers start: 8 outliers final: 6 residues processed: 72 average time/residue: 0.8535 time to fit residues: 80.0383 Evaluate side-chains 70 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 1.402 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 266 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 48 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.059379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.045385 restraints weight = 167384.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.046898 restraints weight = 87066.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.048007 restraints weight = 54900.596| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 7551 Z= 0.254 Angle : 0.668 10.419 10294 Z= 0.334 Chirality : 0.046 0.456 1159 Planarity : 0.004 0.037 1322 Dihedral : 8.845 76.510 1364 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.05 % Allowed : 10.77 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.27), residues: 919 helix: 0.26 (0.46), residues: 122 sheet: -0.03 (0.34), residues: 240 loop : -1.39 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 129 HIS 0.008 0.001 HIS B 192 PHE 0.042 0.002 PHE B 223 TYR 0.021 0.002 TYR B 318 ARG 0.009 0.001 ARG B 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 5) link_NAG-ASN : angle 2.50178 ( 15) link_BETA1-4 : bond 0.00589 ( 10) link_BETA1-4 : angle 2.43443 ( 30) hydrogen bonds : bond 0.03967 ( 253) hydrogen bonds : angle 5.98041 ( 660) link_BETA1-6 : bond 0.00216 ( 1) link_BETA1-6 : angle 1.56511 ( 3) SS BOND : bond 0.00207 ( 15) SS BOND : angle 0.71187 ( 30) covalent geometry : bond 0.00508 ( 7520) covalent geometry : angle 0.64845 (10216) *********************** 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: 16 poor density : 62 time to evaluate : 1.623 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 48 GLU cc_start: 0.9040 (tp30) cc_final: 0.8399 (tp30) REVERT: A 49 GLU cc_start: 0.9416 (pt0) cc_final: 0.8993 (pm20) REVERT: A 71 ASP cc_start: 0.9006 (m-30) cc_final: 0.8241 (t0) REVERT: A 235 TRP cc_start: 0.9154 (t60) cc_final: 0.8629 (t60) REVERT: A 393 LEU cc_start: 0.9177 (tp) cc_final: 0.8968 (tp) REVERT: B 22 MET cc_start: 0.9623 (mmm) cc_final: 0.9314 (ppp) REVERT: B 142 MET cc_start: 0.9345 (mmm) cc_final: 0.8773 (mmm) REVERT: B 266 VAL cc_start: 0.6928 (OUTLIER) cc_final: 0.6635 (p) outliers start: 16 outliers final: 12 residues processed: 75 average time/residue: 0.7099 time to fit residues: 70.3803 Evaluate side-chains 72 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 239 VAL 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 138 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 25 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.060353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.046540 restraints weight = 172714.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.048267 restraints weight = 86291.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.049406 restraints weight = 51874.031| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7551 Z= 0.137 Angle : 0.586 10.662 10294 Z= 0.286 Chirality : 0.046 0.458 1159 Planarity : 0.004 0.036 1322 Dihedral : 8.398 73.221 1362 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.03 % Allowed : 12.56 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.28), residues: 919 helix: 0.72 (0.48), residues: 124 sheet: 0.07 (0.35), residues: 232 loop : -1.26 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 129 HIS 0.005 0.001 HIS A 291 PHE 0.030 0.001 PHE B 223 TYR 0.015 0.001 TYR A 380 ARG 0.003 0.000 ARG A 335 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 5) link_NAG-ASN : angle 2.30789 ( 15) link_BETA1-4 : bond 0.00627 ( 10) link_BETA1-4 : angle 2.34966 ( 30) hydrogen bonds : bond 0.03268 ( 253) hydrogen bonds : angle 5.76623 ( 660) link_BETA1-6 : bond 0.00406 ( 1) link_BETA1-6 : angle 1.47269 ( 3) SS BOND : bond 0.00459 ( 15) SS BOND : angle 1.01718 ( 30) covalent geometry : bond 0.00290 ( 7520) covalent geometry : angle 0.56399 (10216) *********************** 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 69 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 1.106 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: 0.9427 (pt0) cc_final: 0.9197 (pm20) REVERT: A 71 ASP cc_start: 0.9030 (m-30) cc_final: 0.8225 (t0) REVERT: A 235 TRP cc_start: 0.9118 (t60) cc_final: 0.8908 (t60) REVERT: B 22 MET cc_start: 0.9620 (mmm) cc_final: 0.9351 (ppp) REVERT: B 142 MET cc_start: 0.9398 (mmm) cc_final: 0.8812 (mmm) REVERT: B 223 PHE cc_start: 0.8103 (m-80) cc_final: 0.7826 (t80) REVERT: B 266 VAL cc_start: 0.6857 (OUTLIER) cc_final: 0.6559 (p) outliers start: 8 outliers final: 7 residues processed: 68 average time/residue: 0.5668 time to fit residues: 48.8574 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 : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 266 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 21 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 11 optimal weight: 0.0670 chunk 39 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.060616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.046867 restraints weight = 171809.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.048585 restraints weight = 85458.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.049639 restraints weight = 51374.754| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4921 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= 0.115 Angle : 0.560 10.648 10294 Z= 0.271 Chirality : 0.046 0.457 1159 Planarity : 0.004 0.037 1322 Dihedral : 8.010 68.265 1362 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.15 % Allowed : 12.69 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.28), residues: 919 helix: 1.10 (0.51), residues: 124 sheet: 0.19 (0.35), residues: 232 loop : -1.17 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 129 HIS 0.006 0.001 HIS A 291 PHE 0.018 0.001 PHE B 308 TYR 0.012 0.001 TYR A 380 ARG 0.003 0.000 ARG A 449 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 5) link_NAG-ASN : angle 2.27704 ( 15) link_BETA1-4 : bond 0.00633 ( 10) link_BETA1-4 : angle 2.32447 ( 30) hydrogen bonds : bond 0.02957 ( 253) hydrogen bonds : angle 5.57713 ( 660) link_BETA1-6 : bond 0.00424 ( 1) link_BETA1-6 : angle 1.41784 ( 3) SS BOND : bond 0.00168 ( 15) SS BOND : angle 0.58844 ( 30) covalent geometry : bond 0.00247 ( 7520) covalent geometry : angle 0.53954 (10216) *********************** 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 71 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 1.612 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: 0.9415 (pt0) cc_final: 0.9186 (pm20) REVERT: A 71 ASP cc_start: 0.9039 (m-30) cc_final: 0.8269 (t0) REVERT: A 235 TRP cc_start: 0.9123 (t60) cc_final: 0.8870 (t60) REVERT: B 22 MET cc_start: 0.9612 (mmm) cc_final: 0.9367 (ppp) REVERT: B 142 MET cc_start: 0.9413 (mmm) cc_final: 0.8824 (mmm) REVERT: B 266 VAL cc_start: 0.6834 (OUTLIER) cc_final: 0.6528 (p) outliers start: 9 outliers final: 8 residues processed: 70 average time/residue: 0.6859 time to fit residues: 60.7840 Evaluate side-chains 70 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 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 Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 58 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 3 optimal weight: 0.1980 chunk 1 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.061056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.047291 restraints weight = 168263.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.049027 restraints weight = 84664.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.050242 restraints weight = 50996.772| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7551 Z= 0.099 Angle : 0.553 10.662 10294 Z= 0.265 Chirality : 0.046 0.457 1159 Planarity : 0.004 0.037 1322 Dihedral : 7.681 63.402 1362 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.77 % Allowed : 13.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.28), residues: 919 helix: 1.29 (0.51), residues: 124 sheet: 0.29 (0.35), residues: 235 loop : -1.11 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 129 HIS 0.005 0.001 HIS A 291 PHE 0.018 0.001 PHE B 308 TYR 0.012 0.001 TYR A 380 ARG 0.002 0.000 ARG A 449 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 5) link_NAG-ASN : angle 2.24725 ( 15) link_BETA1-4 : bond 0.00640 ( 10) link_BETA1-4 : angle 2.30114 ( 30) hydrogen bonds : bond 0.02780 ( 253) hydrogen bonds : angle 5.43733 ( 660) link_BETA1-6 : bond 0.00466 ( 1) link_BETA1-6 : angle 1.34727 ( 3) SS BOND : bond 0.00111 ( 15) SS BOND : angle 0.49941 ( 30) covalent geometry : bond 0.00220 ( 7520) covalent geometry : angle 0.53319 (10216) *********************** 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 71 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 1.421 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 48 GLU cc_start: 0.8927 (tp30) cc_final: 0.8166 (tp30) REVERT: A 49 GLU cc_start: 0.9454 (pt0) cc_final: 0.9113 (pm20) REVERT: A 71 ASP cc_start: 0.9077 (m-30) cc_final: 0.8285 (t0) REVERT: A 235 TRP cc_start: 0.9127 (t60) cc_final: 0.8887 (t60) REVERT: B 22 MET cc_start: 0.9608 (mmm) cc_final: 0.9381 (ppp) REVERT: B 142 MET cc_start: 0.9400 (mmm) cc_final: 0.8819 (mmm) outliers start: 6 outliers final: 5 residues processed: 70 average time/residue: 0.7267 time to fit residues: 68.9851 Evaluate side-chains 67 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 3.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 306 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 12 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 33 optimal weight: 0.3980 chunk 53 optimal weight: 7.9990 chunk 13 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.059458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.045242 restraints weight = 164479.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.046739 restraints weight = 86527.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.047724 restraints weight = 53447.368| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7551 Z= 0.163 Angle : 0.583 10.659 10294 Z= 0.286 Chirality : 0.045 0.456 1159 Planarity : 0.004 0.036 1322 Dihedral : 7.549 62.262 1359 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 1.03 % Allowed : 13.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.28), residues: 919 helix: 1.16 (0.50), residues: 124 sheet: 0.21 (0.35), residues: 233 loop : -1.14 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 129 HIS 0.004 0.001 HIS B 192 PHE 0.018 0.001 PHE B 223 TYR 0.016 0.001 TYR B 318 ARG 0.003 0.000 ARG A 449 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 5) link_NAG-ASN : angle 2.28698 ( 15) link_BETA1-4 : bond 0.00602 ( 10) link_BETA1-4 : angle 2.31153 ( 30) hydrogen bonds : bond 0.03128 ( 253) hydrogen bonds : angle 5.52385 ( 660) link_BETA1-6 : bond 0.00343 ( 1) link_BETA1-6 : angle 1.49698 ( 3) SS BOND : bond 0.00150 ( 15) SS BOND : angle 0.56154 ( 30) covalent geometry : bond 0.00336 ( 7520) covalent geometry : angle 0.56355 (10216) *********************** 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 71 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 1.092 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: A 48 GLU cc_start: 0.9017 (tp30) cc_final: 0.8385 (tp30) REVERT: A 49 GLU cc_start: 0.9437 (pt0) cc_final: 0.9064 (pm20) REVERT: A 71 ASP cc_start: 0.9045 (m-30) cc_final: 0.8251 (t0) REVERT: A 166 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.8600 (m-80) REVERT: B 22 MET cc_start: 0.9617 (mmm) cc_final: 0.9365 (ppp) REVERT: B 142 MET cc_start: 0.9406 (mmm) cc_final: 0.8805 (mmm) REVERT: B 223 PHE cc_start: 0.7876 (m-80) cc_final: 0.7656 (t80) outliers start: 8 outliers final: 7 residues processed: 70 average time/residue: 0.5668 time to fit residues: 50.6076 Evaluate side-chains 69 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 72 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.057423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.043127 restraints weight = 165701.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.044576 restraints weight = 89312.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.045373 restraints weight = 56040.155| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.6085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7551 Z= 0.230 Angle : 0.659 10.832 10294 Z= 0.333 Chirality : 0.046 0.460 1159 Planarity : 0.004 0.037 1322 Dihedral : 7.774 59.384 1359 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 1.15 % Allowed : 13.46 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.28), residues: 919 helix: 0.24 (0.45), residues: 129 sheet: -0.03 (0.35), residues: 238 loop : -1.36 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 100 HIS 0.007 0.001 HIS B 192 PHE 0.016 0.002 PHE A 244 TYR 0.031 0.002 TYR A 274 ARG 0.005 0.001 ARG A 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 5) link_NAG-ASN : angle 2.28734 ( 15) link_BETA1-4 : bond 0.00553 ( 10) link_BETA1-4 : angle 2.27678 ( 30) hydrogen bonds : bond 0.03696 ( 253) hydrogen bonds : angle 5.95163 ( 660) link_BETA1-6 : bond 0.00289 ( 1) link_BETA1-6 : angle 1.46482 ( 3) SS BOND : bond 0.00229 ( 15) SS BOND : angle 0.80480 ( 30) covalent geometry : bond 0.00465 ( 7520) covalent geometry : angle 0.64185 (10216) ********************** 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 71 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 1.086 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: A 71 ASP cc_start: 0.9097 (m-30) cc_final: 0.8188 (t0) REVERT: A 168 GLU cc_start: 0.9053 (mp0) cc_final: 0.8722 (mp0) REVERT: B 22 MET cc_start: 0.9652 (mmm) cc_final: 0.9412 (ppp) REVERT: B 142 MET cc_start: 0.9387 (mmm) cc_final: 0.8747 (mmm) outliers start: 9 outliers final: 8 residues processed: 70 average time/residue: 0.5297 time to fit residues: 47.6884 Evaluate side-chains 69 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 58 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.058994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.045256 restraints weight = 173058.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.046933 restraints weight = 86372.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.048029 restraints weight = 51835.267| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7551 Z= 0.111 Angle : 0.583 10.956 10294 Z= 0.284 Chirality : 0.046 0.460 1159 Planarity : 0.004 0.055 1322 Dihedral : 7.658 56.098 1359 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.77 % Allowed : 13.85 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.28), residues: 919 helix: 1.12 (0.50), residues: 124 sheet: 0.07 (0.35), residues: 238 loop : -1.21 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 260 HIS 0.004 0.001 HIS A 291 PHE 0.015 0.001 PHE B 308 TYR 0.016 0.001 TYR A 274 ARG 0.003 0.000 ARG A 153 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 5) link_NAG-ASN : angle 2.19963 ( 15) link_BETA1-4 : bond 0.00598 ( 10) link_BETA1-4 : angle 2.17964 ( 30) hydrogen bonds : bond 0.02914 ( 253) hydrogen bonds : angle 5.62538 ( 660) link_BETA1-6 : bond 0.00496 ( 1) link_BETA1-6 : angle 1.35026 ( 3) SS BOND : bond 0.00147 ( 15) SS BOND : angle 0.61366 ( 30) covalent geometry : bond 0.00247 ( 7520) covalent geometry : angle 0.56556 (10216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5887.86 seconds wall clock time: 105 minutes 41.69 seconds (6341.69 seconds total)