Starting phenix.real_space_refine on Sun Nov 17 20:00:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9der_46794/11_2024/9der_46794_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9der_46794/11_2024/9der_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9der_46794/11_2024/9der_46794.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9der_46794/11_2024/9der_46794.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9der_46794/11_2024/9der_46794_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9der_46794/11_2024/9der_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 7.16, per 1000 atoms: 0.50 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: 4.10 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: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 227 through 231 Processing helix chain 'B' and resid 12 through 19 Processing helix chain 'B' and resid 31 through 35 removed outlier: 3.982A pdb=" N GLY B 34 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 Processing helix chain 'B' and resid 123 through 146 removed outlier: 4.429A pdb=" N ASP B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TRP B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N SER B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 175 removed outlier: 4.141A pdb=" N GLU B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 210 Processing helix chain 'B' and resid 221 through 232 removed outlier: 3.799A pdb=" N ALA B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 removed outlier: 4.169A pdb=" N ALA B 263 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 287 removed outlier: 4.361A pdb=" N THR B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 303 Processing helix chain 'B' and resid 314 through 325 removed outlier: 3.779A pdb=" N TYR B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.900A pdb=" N LEU B 343 " --> pdb=" O ASN B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 441 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 11 Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 27 removed outlier: 3.634A pdb=" N SER A 22 " --> pdb=" O GLY A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 79 Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 100 removed outlier: 3.739A pdb=" N SER A 96 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 175 Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 242 removed outlier: 6.773A pdb=" N VAL A 267 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG A 279 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A 269 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 293 through 296 Processing sheet with id=AA8, first strand: chain 'A' and resid 314 through 315 Processing sheet with id=AA9, first strand: chain 'A' and resid 360 through 362 removed outlier: 3.565A pdb=" N GLN A 405 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 61 through 65 removed outlier: 6.252A pdb=" N ARG B 87 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 83 through 84 Processing sheet with id=AB3, first strand: chain 'B' and resid 190 through 197 removed outlier: 6.525A pdb=" N VAL B 193 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ALA B 155 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N THR B 195 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N PHE B 153 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP B 119 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR B 250 " --> pdb=" O ALA B 309 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 454 through 456 253 hydrogen bonds defined for protein. 660 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.19 Time building geometry restraints manager: 4.78 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: 1.060 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: 0.250 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 34.520 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7520 Z= 0.180 Angle : 0.565 10.574 10216 Z= 0.242 Chirality : 0.052 0.467 1159 Planarity : 0.003 0.028 1322 Dihedral : 15.299 113.836 3011 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.90 % Allowed : 4.62 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.28), residues: 919 helix: 0.51 (0.51), residues: 126 sheet: 0.95 (0.33), residues: 254 loop : -0.89 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP B 466 HIS 0.002 0.000 HIS B 255 PHE 0.008 0.001 PHE B 414 TYR 0.007 0.001 TYR B 318 ARG 0.002 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 1.175 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: 0.5811 time to fit residues: 105.0640 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 : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 406 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 134 GLN A 333 GLN A 444 GLN ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 7520 Z= 0.328 Angle : 0.691 10.217 10216 Z= 0.341 Chirality : 0.048 0.450 1159 Planarity : 0.005 0.066 1322 Dihedral : 13.603 84.095 1365 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.28 % Allowed : 9.87 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.28), residues: 919 helix: 0.46 (0.49), residues: 123 sheet: 0.51 (0.33), residues: 251 loop : -1.00 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 129 HIS 0.008 0.001 HIS A 112 PHE 0.024 0.002 PHE B 308 TYR 0.019 0.001 TYR B 318 ARG 0.005 0.001 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 94 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 1.191 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: 0.9034 (tp30) cc_final: 0.8364 (tp30) REVERT: A 49 GLU cc_start: 0.9516 (pt0) cc_final: 0.8979 (pm20) REVERT: A 71 ASP cc_start: 0.8909 (m-30) cc_final: 0.8137 (t0) REVERT: A 235 TRP cc_start: 0.8884 (t60) cc_final: 0.8347 (t60) REVERT: A 420 SER cc_start: 0.9118 (t) cc_final: 0.8815 (p) REVERT: B 282 SER cc_start: 0.9220 (m) cc_final: 0.8874 (p) outliers start: 10 outliers final: 8 residues processed: 91 average time/residue: 0.5839 time to fit residues: 66.7858 Evaluate side-chains 84 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 9.9990 chunk 25 optimal weight: 0.3980 chunk 68 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 82 optimal weight: 0.3980 chunk 89 optimal weight: 6.9990 chunk 73 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7520 Z= 0.156 Angle : 0.574 10.531 10216 Z= 0.272 Chirality : 0.048 0.453 1159 Planarity : 0.004 0.041 1322 Dihedral : 10.776 80.271 1365 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.77 % Allowed : 10.90 % Favored : 88.33 % 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: -0.37 (0.28), residues: 919 helix: 0.94 (0.51), residues: 123 sheet: 0.62 (0.34), residues: 241 loop : -0.94 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 129 HIS 0.003 0.001 HIS A 112 PHE 0.026 0.001 PHE B 308 TYR 0.012 0.001 TYR A 380 ARG 0.002 0.000 ARG A 90 *********************** 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 82 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 1.188 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: 0.8957 (tp30) cc_final: 0.8175 (tp30) REVERT: A 49 GLU cc_start: 0.9488 (pt0) cc_final: 0.8932 (pm20) REVERT: A 71 ASP cc_start: 0.8850 (m-30) cc_final: 0.8139 (t0) REVERT: A 168 GLU cc_start: 0.8856 (mp0) cc_final: 0.8338 (mp0) REVERT: A 420 SER cc_start: 0.8984 (t) cc_final: 0.8707 (p) REVERT: B 282 SER cc_start: 0.9198 (m) cc_final: 0.8814 (p) outliers start: 6 outliers final: 5 residues processed: 80 average time/residue: 0.5883 time to fit residues: 60.1342 Evaluate side-chains 79 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 406 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 6.9990 chunk 42 optimal weight: 0.0170 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 87 optimal weight: 30.0000 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 overall best weight: 4.8026 ------------------------------------------------------------------------------- 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** ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 7520 Z= 0.472 Angle : 0.807 10.101 10216 Z= 0.418 Chirality : 0.048 0.448 1159 Planarity : 0.006 0.061 1322 Dihedral : 9.547 81.243 1365 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 26.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.05 % Favored : 91.84 % Rotamer: Outliers : 1.67 % Allowed : 10.51 % Favored : 87.82 % 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: -1.70 (0.26), residues: 919 helix: -1.09 (0.40), residues: 127 sheet: -0.13 (0.33), residues: 238 loop : -1.65 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 162 HIS 0.011 0.002 HIS B 192 PHE 0.060 0.003 PHE B 223 TYR 0.032 0.003 TYR B 318 ARG 0.007 0.001 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 1.178 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 48 GLU cc_start: 0.9309 (tp30) cc_final: 0.8599 (tm-30) REVERT: A 49 GLU cc_start: 0.9479 (pt0) cc_final: 0.9174 (pm20) REVERT: A 71 ASP cc_start: 0.9039 (m-30) cc_final: 0.8218 (t0) REVERT: A 168 GLU cc_start: 0.9025 (mp0) cc_final: 0.8613 (mp0) REVERT: A 235 TRP cc_start: 0.9149 (t60) cc_final: 0.8739 (t60) REVERT: B 22 MET cc_start: 0.9646 (mmm) cc_final: 0.9398 (ppp) REVERT: B 142 MET cc_start: 0.9369 (mmm) cc_final: 0.8798 (mmm) REVERT: B 266 VAL cc_start: 0.6865 (OUTLIER) cc_final: 0.6581 (p) outliers start: 13 outliers final: 8 residues processed: 72 average time/residue: 0.5736 time to fit residues: 52.4290 Evaluate side-chains 65 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 288 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.0020 chunk 1 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 372 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7520 Z= 0.176 Angle : 0.581 10.720 10216 Z= 0.289 Chirality : 0.046 0.458 1159 Planarity : 0.004 0.037 1322 Dihedral : 8.674 76.427 1362 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.15 % Allowed : 11.92 % Favored : 86.92 % 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: -1.02 (0.27), residues: 919 helix: 0.53 (0.49), residues: 123 sheet: 0.07 (0.34), residues: 233 loop : -1.34 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 260 HIS 0.005 0.001 HIS A 291 PHE 0.021 0.001 PHE B 223 TYR 0.027 0.002 TYR A 329 ARG 0.005 0.000 ARG A 208 *********************** 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 71 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 1.247 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 49 GLU cc_start: 0.9447 (pt0) cc_final: 0.9159 (pm20) REVERT: A 71 ASP cc_start: 0.8998 (m-30) cc_final: 0.8220 (t0) REVERT: B 66 ASP cc_start: 0.8970 (p0) cc_final: 0.8546 (p0) REVERT: B 266 VAL cc_start: 0.6686 (OUTLIER) cc_final: 0.6340 (p) outliers start: 9 outliers final: 6 residues processed: 69 average time/residue: 0.5596 time to fit residues: 49.7462 Evaluate side-chains 64 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 266 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7520 Z= 0.231 Angle : 0.581 10.562 10216 Z= 0.289 Chirality : 0.045 0.455 1159 Planarity : 0.004 0.037 1322 Dihedral : 8.331 73.029 1362 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 1.41 % Allowed : 12.44 % 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: -0.98 (0.27), residues: 919 helix: 0.68 (0.49), residues: 124 sheet: 0.09 (0.34), residues: 233 loop : -1.34 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 129 HIS 0.004 0.001 HIS A 291 PHE 0.028 0.002 PHE B 223 TYR 0.015 0.001 TYR B 318 ARG 0.003 0.000 ARG A 449 *********************** 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 66 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 1.205 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: A 49 GLU cc_start: 0.9492 (pt0) cc_final: 0.9247 (pm20) REVERT: A 71 ASP cc_start: 0.9007 (m-30) cc_final: 0.8221 (t0) REVERT: A 166 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.8104 (m-80) REVERT: A 168 GLU cc_start: 0.9090 (mp0) cc_final: 0.8660 (mp0) REVERT: B 142 MET cc_start: 0.9370 (mmm) cc_final: 0.8748 (mmm) REVERT: B 223 PHE cc_start: 0.7792 (m-80) cc_final: 0.7416 (t80) REVERT: B 266 VAL cc_start: 0.6766 (OUTLIER) cc_final: 0.6459 (p) outliers start: 11 outliers final: 8 residues processed: 65 average time/residue: 0.5588 time to fit residues: 46.7510 Evaluate side-chains 65 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 35 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7520 Z= 0.183 Angle : 0.557 10.648 10216 Z= 0.275 Chirality : 0.046 0.459 1159 Planarity : 0.004 0.037 1322 Dihedral : 8.068 67.565 1362 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % 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: -0.84 (0.28), residues: 919 helix: 1.02 (0.50), residues: 124 sheet: 0.16 (0.35), residues: 227 loop : -1.27 (0.26), residues: 568 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 0.014 0.001 TYR A 380 ARG 0.008 0.000 ARG B 67 *********************** 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 65 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 1.185 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 49 GLU cc_start: 0.9485 (pt0) cc_final: 0.9233 (pm20) REVERT: A 71 ASP cc_start: 0.8978 (m-30) cc_final: 0.8200 (t0) REVERT: A 166 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.8072 (m-80) REVERT: A 168 GLU cc_start: 0.8984 (mp0) cc_final: 0.8597 (mp0) REVERT: B 22 MET cc_start: 0.9668 (mmm) cc_final: 0.9386 (ppp) outliers start: 9 outliers final: 7 residues processed: 64 average time/residue: 0.5570 time to fit residues: 45.9205 Evaluate side-chains 65 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 138 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 84 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.5332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7520 Z= 0.201 Angle : 0.560 10.650 10216 Z= 0.276 Chirality : 0.045 0.456 1159 Planarity : 0.004 0.037 1322 Dihedral : 7.770 64.100 1361 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.41 % Allowed : 12.95 % 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: -0.80 (0.28), residues: 919 helix: 1.02 (0.50), residues: 124 sheet: 0.15 (0.35), residues: 227 loop : -1.22 (0.26), residues: 568 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 0.020 0.001 PHE B 308 TYR 0.014 0.001 TYR B 318 ARG 0.004 0.000 ARG A 208 *********************** 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 70 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 1.208 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: A 49 GLU cc_start: 0.9487 (pt0) cc_final: 0.9240 (pm20) REVERT: A 71 ASP cc_start: 0.8992 (m-30) cc_final: 0.8202 (t0) REVERT: A 166 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.8088 (m-80) REVERT: A 168 GLU cc_start: 0.9060 (mp0) cc_final: 0.8669 (mp0) REVERT: B 22 MET cc_start: 0.9660 (mmm) cc_final: 0.9384 (ppp) REVERT: B 142 MET cc_start: 0.9394 (mmm) cc_final: 0.8773 (mmm) REVERT: B 223 PHE cc_start: 0.7820 (m-80) cc_final: 0.7509 (t80) outliers start: 11 outliers final: 10 residues processed: 67 average time/residue: 0.5520 time to fit residues: 47.8900 Evaluate side-chains 67 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 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 295 MET Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7520 Z= 0.197 Angle : 0.562 10.720 10216 Z= 0.278 Chirality : 0.045 0.457 1159 Planarity : 0.004 0.037 1322 Dihedral : 7.645 62.203 1361 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.41 % Allowed : 12.95 % 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: -0.80 (0.28), residues: 919 helix: 0.97 (0.49), residues: 123 sheet: 0.16 (0.35), residues: 227 loop : -1.22 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 129 HIS 0.004 0.001 HIS A 291 PHE 0.018 0.001 PHE B 308 TYR 0.013 0.001 TYR B 318 ARG 0.003 0.000 ARG A 208 *********************** 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 68 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 1.200 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: A 49 GLU cc_start: 0.9504 (pt0) cc_final: 0.9268 (pm20) REVERT: A 71 ASP cc_start: 0.9026 (m-30) cc_final: 0.8244 (t0) REVERT: A 166 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.8077 (m-80) REVERT: A 168 GLU cc_start: 0.9030 (mp0) cc_final: 0.8632 (mp0) REVERT: B 22 MET cc_start: 0.9654 (mmm) cc_final: 0.9379 (ppp) REVERT: B 223 PHE cc_start: 0.7723 (m-80) cc_final: 0.7515 (t80) outliers start: 11 outliers final: 10 residues processed: 65 average time/residue: 0.5586 time to fit residues: 46.7546 Evaluate side-chains 68 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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 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 295 MET 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 41 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 7 optimal weight: 0.4980 chunk 55 optimal weight: 10.0000 chunk 44 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7520 Z= 0.150 Angle : 0.542 10.752 10216 Z= 0.265 Chirality : 0.046 0.457 1159 Planarity : 0.004 0.036 1322 Dihedral : 7.367 58.849 1361 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.90 % Allowed : 13.59 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.28), residues: 919 helix: 1.25 (0.51), residues: 123 sheet: 0.24 (0.35), residues: 227 loop : -1.13 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 260 HIS 0.005 0.001 HIS A 291 PHE 0.020 0.001 PHE B 308 TYR 0.011 0.001 TYR A 380 ARG 0.004 0.000 ARG A 208 ********************** 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 65 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 1.233 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: A 48 GLU cc_start: 0.9101 (tp30) cc_final: 0.8350 (tp30) REVERT: A 49 GLU cc_start: 0.9477 (pt0) cc_final: 0.9128 (pm20) REVERT: A 71 ASP cc_start: 0.9006 (m-30) cc_final: 0.8244 (t0) REVERT: A 166 TYR cc_start: 0.8753 (OUTLIER) cc_final: 0.8010 (m-80) REVERT: A 168 GLU cc_start: 0.8974 (mp0) cc_final: 0.8599 (mp0) REVERT: B 22 MET cc_start: 0.9645 (mmm) cc_final: 0.9368 (ppp) outliers start: 7 outliers final: 5 residues processed: 64 average time/residue: 0.5706 time to fit residues: 46.7510 Evaluate side-chains 63 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 295 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.058143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.043747 restraints weight = 166367.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.045114 restraints weight = 90369.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.046080 restraints weight = 55846.293| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 7520 Z= 0.290 Angle : 0.610 10.702 10216 Z= 0.309 Chirality : 0.045 0.458 1159 Planarity : 0.004 0.036 1322 Dihedral : 7.470 58.861 1359 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 1.15 % Allowed : 13.21 % 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: -0.96 (0.28), residues: 919 helix: 0.47 (0.46), residues: 129 sheet: 0.05 (0.35), residues: 234 loop : -1.25 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 129 HIS 0.006 0.001 HIS B 192 PHE 0.016 0.002 PHE B 308 TYR 0.020 0.002 TYR B 318 ARG 0.003 0.001 ARG A 449 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3412.25 seconds wall clock time: 61 minutes 40.09 seconds (3700.09 seconds total)