Starting phenix.real_space_refine on Tue Jan 14 23:33:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vch_43136/01_2025/8vch_43136.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vch_43136/01_2025/8vch_43136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vch_43136/01_2025/8vch_43136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vch_43136/01_2025/8vch_43136.map" model { file = "/net/cci-nas-00/data/ceres_data/8vch_43136/01_2025/8vch_43136.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vch_43136/01_2025/8vch_43136.cif" } resolution = 2.55 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= 0.002 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: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 32 5.16 5 C 5104 2.51 5 N 1192 2.21 5 O 1284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 7614 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1903 Classifications: {'peptide': 253} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 239} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1903 Classifications: {'peptide': 253} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 239} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "C" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1903 Classifications: {'peptide': 253} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 239} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "D" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1903 Classifications: {'peptide': 253} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 239} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.18, per 1000 atoms: 0.68 Number of scatterers: 7614 At special positions: 0 Unit cell: (101.46, 101.46, 71.556, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 2 19.00 S 32 16.00 O 1284 8.00 N 1192 7.00 C 5104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 1.1 seconds 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1864 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 145 through 155 Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 159 through 184 removed outlier: 4.195A pdb=" N THR A 184 " --> pdb=" O PHE A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 244 Processing helix chain 'A' and resid 249 through 252 Processing helix chain 'A' and resid 253 through 262 removed outlier: 3.729A pdb=" N ASP A 259 " --> pdb=" O MET A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 275 removed outlier: 3.680A pdb=" N PHE A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 300 Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 311 through 324 Processing helix chain 'A' and resid 324 through 350 Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 373 Processing helix chain 'A' and resid 384 through 403 removed outlier: 3.642A pdb=" N VAL A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.669A pdb=" N ILE A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 159 through 184 removed outlier: 4.125A pdb=" N THR B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 244 Processing helix chain 'B' and resid 253 through 262 removed outlier: 3.872A pdb=" N ASP B 259 " --> pdb=" O MET B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 275 removed outlier: 3.620A pdb=" N PHE B 267 " --> pdb=" O ILE B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 300 removed outlier: 3.560A pdb=" N ARG B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 310 Processing helix chain 'B' and resid 311 through 324 Processing helix chain 'B' and resid 324 through 350 Processing helix chain 'B' and resid 361 through 363 No H-bonds generated for 'chain 'B' and resid 361 through 363' Processing helix chain 'B' and resid 364 through 373 Processing helix chain 'B' and resid 384 through 403 removed outlier: 3.660A pdb=" N VAL B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 419 removed outlier: 3.651A pdb=" N ILE B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 155 Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 159 through 184 removed outlier: 3.610A pdb=" N ARG C 163 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR C 184 " --> pdb=" O PHE C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 244 Processing helix chain 'C' and resid 249 through 252 Processing helix chain 'C' and resid 253 through 262 removed outlier: 3.700A pdb=" N ASP C 259 " --> pdb=" O MET C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 275 removed outlier: 3.605A pdb=" N PHE C 267 " --> pdb=" O ILE C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 300 removed outlier: 3.534A pdb=" N ARG C 300 " --> pdb=" O ILE C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 310 Processing helix chain 'C' and resid 311 through 324 Processing helix chain 'C' and resid 324 through 350 Processing helix chain 'C' and resid 361 through 363 No H-bonds generated for 'chain 'C' and resid 361 through 363' Processing helix chain 'C' and resid 364 through 373 Processing helix chain 'C' and resid 384 through 403 removed outlier: 3.661A pdb=" N VAL C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 419 removed outlier: 3.698A pdb=" N ILE C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 156 through 158 No H-bonds generated for 'chain 'D' and resid 156 through 158' Processing helix chain 'D' and resid 159 through 184 removed outlier: 4.154A pdb=" N THR D 184 " --> pdb=" O PHE D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 244 Processing helix chain 'D' and resid 253 through 262 removed outlier: 3.732A pdb=" N ASP D 259 " --> pdb=" O MET D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 275 removed outlier: 3.649A pdb=" N PHE D 267 " --> pdb=" O ILE D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 300 Processing helix chain 'D' and resid 301 through 310 Processing helix chain 'D' and resid 311 through 324 Processing helix chain 'D' and resid 324 through 350 Processing helix chain 'D' and resid 361 through 363 No H-bonds generated for 'chain 'D' and resid 361 through 363' Processing helix chain 'D' and resid 364 through 373 Processing helix chain 'D' and resid 384 through 403 removed outlier: 3.614A pdb=" N VAL D 399 " --> pdb=" O ALA D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 419 removed outlier: 3.518A pdb=" N ILE D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) 559 hydrogen bonds defined for protein. 1587 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: 2.15 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2296 1.34 - 1.46: 1835 1.46 - 1.58: 3625 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 7804 Sorted by residual: bond pdb=" CB VAL C 370 " pdb=" CG1 VAL C 370 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.53e+00 bond pdb=" CB VAL A 370 " pdb=" CG1 VAL A 370 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.41e+00 bond pdb=" CB GLU C 273 " pdb=" CG GLU C 273 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.39e+00 bond pdb=" CB VAL D 370 " pdb=" CG1 VAL D 370 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.34e+00 bond pdb=" CB VAL B 370 " pdb=" CG1 VAL B 370 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.33e+00 ... (remaining 7799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 10152 1.16 - 2.33: 363 2.33 - 3.49: 71 3.49 - 4.66: 32 4.66 - 5.82: 10 Bond angle restraints: 10628 Sorted by residual: angle pdb=" N ILE D 263 " pdb=" CA ILE D 263 " pdb=" C ILE D 263 " ideal model delta sigma weight residual 113.42 108.53 4.89 1.17e+00 7.31e-01 1.75e+01 angle pdb=" N ILE B 263 " pdb=" CA ILE B 263 " pdb=" C ILE B 263 " ideal model delta sigma weight residual 113.42 108.70 4.72 1.17e+00 7.31e-01 1.63e+01 angle pdb=" N ILE C 263 " pdb=" CA ILE C 263 " pdb=" C ILE C 263 " ideal model delta sigma weight residual 113.42 108.89 4.53 1.17e+00 7.31e-01 1.50e+01 angle pdb=" N ILE A 263 " pdb=" CA ILE A 263 " pdb=" C ILE A 263 " ideal model delta sigma weight residual 113.42 109.04 4.38 1.17e+00 7.31e-01 1.40e+01 angle pdb=" CA GLU C 273 " pdb=" CB GLU C 273 " pdb=" CG GLU C 273 " ideal model delta sigma weight residual 114.10 119.92 -5.82 2.00e+00 2.50e-01 8.47e+00 ... (remaining 10623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 3885 16.47 - 32.94: 429 32.94 - 49.40: 125 49.40 - 65.87: 15 65.87 - 82.34: 6 Dihedral angle restraints: 4460 sinusoidal: 1572 harmonic: 2888 Sorted by residual: dihedral pdb=" CG ARG B 309 " pdb=" CD ARG B 309 " pdb=" NE ARG B 309 " pdb=" CZ ARG B 309 " ideal model delta sinusoidal sigma weight residual -180.00 -137.90 -42.10 2 1.50e+01 4.44e-03 9.59e+00 dihedral pdb=" CB MET A 372 " pdb=" CG MET A 372 " pdb=" SD MET A 372 " pdb=" CE MET A 372 " ideal model delta sinusoidal sigma weight residual -60.00 -1.12 -58.88 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB MET A 325 " pdb=" CG MET A 325 " pdb=" SD MET A 325 " pdb=" CE MET A 325 " ideal model delta sinusoidal sigma weight residual 180.00 121.72 58.28 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 4457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 589 0.023 - 0.047: 358 0.047 - 0.070: 213 0.070 - 0.094: 78 0.094 - 0.117: 38 Chirality restraints: 1276 Sorted by residual: chirality pdb=" CA PRO A 407 " pdb=" N PRO A 407 " pdb=" C PRO A 407 " pdb=" CB PRO A 407 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.44e-01 chirality pdb=" CA PRO C 407 " pdb=" N PRO C 407 " pdb=" C PRO C 407 " pdb=" CB PRO C 407 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.42e-01 chirality pdb=" CA ASP C 355 " pdb=" N ASP C 355 " pdb=" C ASP C 355 " pdb=" CB ASP C 355 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.39e-01 ... (remaining 1273 not shown) Planarity restraints: 1308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 160 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO A 161 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 160 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO D 161 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 161 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 161 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 160 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO B 161 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 161 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 161 " -0.021 5.00e-02 4.00e+02 ... (remaining 1305 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.84: 2656 2.84 - 3.41: 8585 3.41 - 3.99: 13935 3.99 - 4.56: 20502 4.56 - 5.14: 28010 Nonbonded interactions: 73688 Sorted by model distance: nonbonded pdb=" OD2 ASP A 352 " pdb=" NH2 ARG B 294 " model vdw 2.260 3.120 nonbonded pdb=" OE1 GLU D 353 " pdb=" OG1 THR D 383 " model vdw 2.282 3.040 nonbonded pdb=" OE1 GLU B 353 " pdb=" OG1 THR B 383 " model vdw 2.302 3.040 nonbonded pdb=" OE1 GLU A 353 " pdb=" OG1 THR A 383 " model vdw 2.319 3.040 nonbonded pdb=" OE1 GLU B 183 " pdb=" NH2 ARG B 300 " model vdw 2.390 3.120 ... (remaining 73683 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 138 through 421) selection = chain 'B' selection = (chain 'C' and resid 138 through 421) selection = chain 'D' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.890 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 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 : 0.004 0.041 7804 Z= 0.229 Angle : 0.578 5.820 10628 Z= 0.335 Chirality : 0.041 0.117 1276 Planarity : 0.004 0.045 1308 Dihedral : 15.042 82.339 2596 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.78 % Allowed : 17.23 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.09 (0.27), residues: 988 helix: 2.03 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -0.36 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 150 HIS 0.002 0.001 HIS A 310 PHE 0.016 0.001 PHE B 153 TYR 0.012 0.002 TYR A 155 ARG 0.005 0.001 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.898 Fit side-chains REVERT: B 260 ILE cc_start: 0.7782 (mt) cc_final: 0.7512 (mp) outliers start: 6 outliers final: 2 residues processed: 110 average time/residue: 1.3491 time to fit residues: 156.2518 Evaluate side-chains 100 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain B residue 419 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 25 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.116648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.082836 restraints weight = 11590.402| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.58 r_work: 0.3108 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7804 Z= 0.229 Angle : 0.505 5.299 10628 Z= 0.266 Chirality : 0.040 0.129 1276 Planarity : 0.005 0.040 1308 Dihedral : 3.571 34.984 1065 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.59 % Allowed : 16.97 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.68 (0.29), residues: 988 helix: 2.27 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.36 (0.44), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 232 HIS 0.002 0.001 HIS B 310 PHE 0.016 0.001 PHE D 336 TYR 0.009 0.001 TYR D 347 ARG 0.004 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.799 Fit side-chains REVERT: A 357 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7691 (mt0) REVERT: C 163 ARG cc_start: 0.7109 (mtp85) cc_final: 0.6901 (mtp85) REVERT: C 183 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7533 (mt-10) REVERT: D 292 ILE cc_start: 0.7455 (pp) cc_final: 0.7064 (pt) outliers start: 20 outliers final: 8 residues processed: 113 average time/residue: 1.2703 time to fit residues: 151.7449 Evaluate side-chains 107 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 325 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 64 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.114955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.082039 restraints weight = 12007.655| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.49 r_work: 0.3087 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7804 Z= 0.232 Angle : 0.497 5.290 10628 Z= 0.259 Chirality : 0.040 0.122 1276 Planarity : 0.004 0.040 1308 Dihedral : 3.242 10.384 1060 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.24 % Allowed : 19.30 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.77 (0.28), residues: 988 helix: 2.37 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.27 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 232 HIS 0.002 0.001 HIS B 310 PHE 0.016 0.001 PHE D 336 TYR 0.008 0.001 TYR B 266 ARG 0.003 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 1.093 Fit side-chains REVERT: A 154 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7885 (tp30) REVERT: A 357 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7745 (mt0) REVERT: C 163 ARG cc_start: 0.7220 (mtp85) cc_final: 0.6998 (mtp85) REVERT: C 183 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7754 (mt-10) outliers start: 25 outliers final: 10 residues processed: 122 average time/residue: 1.4022 time to fit residues: 180.5700 Evaluate side-chains 111 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 325 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 12 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 55 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 86 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.115447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.082600 restraints weight = 11778.629| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.47 r_work: 0.3102 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7804 Z= 0.189 Angle : 0.478 5.209 10628 Z= 0.248 Chirality : 0.039 0.120 1276 Planarity : 0.004 0.040 1308 Dihedral : 3.192 11.221 1060 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.37 % Allowed : 19.82 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.91 (0.28), residues: 988 helix: 2.48 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.27 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 232 HIS 0.001 0.000 HIS B 310 PHE 0.012 0.001 PHE B 336 TYR 0.010 0.001 TYR C 155 ARG 0.003 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.892 Fit side-chains REVERT: A 154 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7809 (tp30) REVERT: A 246 SER cc_start: 0.8232 (OUTLIER) cc_final: 0.7781 (m) REVERT: A 357 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7591 (mt0) REVERT: B 300 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7039 (mtp85) REVERT: B 322 LYS cc_start: 0.7506 (mttp) cc_final: 0.7291 (mptt) REVERT: B 380 MET cc_start: 0.8273 (tmm) cc_final: 0.8022 (tmt) REVERT: C 163 ARG cc_start: 0.7194 (mtp85) cc_final: 0.6898 (mmm160) REVERT: C 183 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7747 (mt-10) REVERT: C 300 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7000 (mtp85) outliers start: 26 outliers final: 8 residues processed: 123 average time/residue: 1.3229 time to fit residues: 171.3775 Evaluate side-chains 115 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 325 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.115017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.082140 restraints weight = 11769.723| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.45 r_work: 0.3092 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7804 Z= 0.208 Angle : 0.486 8.535 10628 Z= 0.249 Chirality : 0.040 0.121 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.172 10.880 1060 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.24 % Allowed : 19.56 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.91 (0.28), residues: 988 helix: 2.47 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.34 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 232 HIS 0.001 0.000 HIS C 310 PHE 0.012 0.001 PHE B 336 TYR 0.010 0.001 TYR D 155 ARG 0.002 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.812 Fit side-chains REVERT: A 154 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7799 (tp30) REVERT: A 326 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7608 (ttt-90) REVERT: A 357 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7756 (mt0) REVERT: B 260 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.8056 (mt) REVERT: B 300 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7117 (mtp85) REVERT: C 163 ARG cc_start: 0.7189 (mtp85) cc_final: 0.6895 (mmm160) REVERT: C 183 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7672 (mt-10) REVERT: C 300 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.6953 (mtp85) outliers start: 25 outliers final: 11 residues processed: 122 average time/residue: 1.3589 time to fit residues: 174.5824 Evaluate side-chains 119 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 325 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 0.2980 chunk 4 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.115535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.082626 restraints weight = 11802.635| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.47 r_work: 0.3104 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7804 Z= 0.176 Angle : 0.475 7.222 10628 Z= 0.244 Chirality : 0.039 0.119 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.125 10.998 1060 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.37 % Allowed : 20.21 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.02 (0.28), residues: 988 helix: 2.54 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.41 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 232 HIS 0.001 0.000 HIS B 310 PHE 0.010 0.001 PHE B 336 TYR 0.010 0.001 TYR B 155 ARG 0.002 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.781 Fit side-chains REVERT: A 154 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7855 (tp30) REVERT: A 292 ILE cc_start: 0.7086 (pp) cc_final: 0.6836 (pp) REVERT: A 326 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7513 (ttt-90) REVERT: A 357 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7625 (mt0) REVERT: B 260 ILE cc_start: 0.8252 (mt) cc_final: 0.8013 (mt) REVERT: B 300 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7207 (mtp85) REVERT: B 380 MET cc_start: 0.8294 (tmm) cc_final: 0.8045 (tmt) REVERT: C 163 ARG cc_start: 0.7202 (mtp85) cc_final: 0.6933 (mmm160) REVERT: C 183 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7660 (mt-10) REVERT: C 300 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.6987 (mtp85) REVERT: D 292 ILE cc_start: 0.7585 (pp) cc_final: 0.7231 (pt) REVERT: D 380 MET cc_start: 0.8192 (tmm) cc_final: 0.7977 (tmt) outliers start: 26 outliers final: 9 residues processed: 126 average time/residue: 1.4380 time to fit residues: 190.2123 Evaluate side-chains 121 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 325 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 53 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.114697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.081699 restraints weight = 11869.143| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.47 r_work: 0.3086 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7804 Z= 0.214 Angle : 0.488 6.883 10628 Z= 0.252 Chirality : 0.040 0.120 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.154 10.795 1060 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.02 % Allowed : 20.47 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.93 (0.28), residues: 988 helix: 2.46 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.42 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 232 HIS 0.001 0.000 HIS B 310 PHE 0.013 0.001 PHE D 336 TYR 0.011 0.001 TYR D 155 ARG 0.002 0.000 ARG C 294 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.791 Fit side-chains REVERT: A 154 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7833 (tp30) REVERT: A 292 ILE cc_start: 0.6847 (pp) cc_final: 0.6592 (pp) REVERT: A 294 ARG cc_start: 0.5699 (mtm180) cc_final: 0.5147 (mmt90) REVERT: A 326 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7526 (ttt-90) REVERT: A 357 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7591 (mt0) REVERT: B 260 ILE cc_start: 0.8193 (mt) cc_final: 0.7956 (mt) REVERT: B 300 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7196 (mtp85) REVERT: C 154 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7732 (tp30) REVERT: C 163 ARG cc_start: 0.7196 (mtp85) cc_final: 0.6914 (mmm160) REVERT: C 183 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7670 (mt-10) REVERT: C 300 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.6969 (mtp85) REVERT: D 251 PHE cc_start: 0.8619 (m-10) cc_final: 0.8257 (m-80) REVERT: D 292 ILE cc_start: 0.7550 (pp) cc_final: 0.7198 (pt) REVERT: D 303 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8147 (ptt-90) REVERT: D 380 MET cc_start: 0.8209 (tmm) cc_final: 0.7965 (tmt) outliers start: 31 outliers final: 12 residues processed: 133 average time/residue: 1.3669 time to fit residues: 191.0631 Evaluate side-chains 127 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 303 ARG Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 325 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 58 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.115209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.082368 restraints weight = 11910.847| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.47 r_work: 0.3100 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7804 Z= 0.179 Angle : 0.481 6.788 10628 Z= 0.248 Chirality : 0.039 0.119 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.118 11.074 1060 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.37 % Allowed : 20.73 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.07 (0.28), residues: 988 helix: 2.56 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.49 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 232 HIS 0.001 0.000 HIS C 310 PHE 0.011 0.001 PHE D 153 TYR 0.010 0.001 TYR B 155 ARG 0.005 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.710 Fit side-chains REVERT: A 154 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7758 (tp30) REVERT: A 292 ILE cc_start: 0.6932 (pp) cc_final: 0.6405 (pt) REVERT: A 294 ARG cc_start: 0.5710 (mtm180) cc_final: 0.5412 (mmt90) REVERT: A 326 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7481 (ttt-90) REVERT: A 357 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7524 (mt0) REVERT: B 300 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7222 (mtp85) REVERT: C 154 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7819 (tp30) REVERT: C 163 ARG cc_start: 0.7164 (mtp85) cc_final: 0.6888 (mmm160) REVERT: C 183 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7651 (mt-10) REVERT: C 300 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.7132 (mtp85) REVERT: D 251 PHE cc_start: 0.8622 (m-10) cc_final: 0.8257 (m-80) REVERT: D 292 ILE cc_start: 0.7551 (pp) cc_final: 0.7206 (pt) REVERT: D 303 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8171 (ptt-90) REVERT: D 380 MET cc_start: 0.8245 (tmm) cc_final: 0.7948 (tmt) outliers start: 26 outliers final: 11 residues processed: 126 average time/residue: 1.3978 time to fit residues: 185.6021 Evaluate side-chains 123 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 303 ARG Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 325 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 37 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 19 optimal weight: 0.2980 chunk 73 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 50 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.115048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.082377 restraints weight = 12090.303| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.48 r_work: 0.3099 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7804 Z= 0.185 Angle : 0.483 6.623 10628 Z= 0.249 Chirality : 0.039 0.118 1276 Planarity : 0.004 0.038 1308 Dihedral : 3.104 10.735 1060 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.37 % Allowed : 20.85 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.07 (0.28), residues: 988 helix: 2.55 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.55 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 232 HIS 0.001 0.000 HIS B 310 PHE 0.011 0.001 PHE C 336 TYR 0.011 0.001 TYR D 155 ARG 0.005 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.798 Fit side-chains REVERT: A 154 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7825 (tp30) REVERT: A 292 ILE cc_start: 0.6930 (pp) cc_final: 0.6414 (pt) REVERT: A 294 ARG cc_start: 0.6018 (mtm180) cc_final: 0.5664 (mmt90) REVERT: A 326 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7476 (ttt-90) REVERT: A 357 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7454 (mt0) REVERT: B 154 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7814 (tp30) REVERT: B 300 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.7229 (mtp85) REVERT: C 154 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7704 (tp30) REVERT: C 163 ARG cc_start: 0.7215 (mtp85) cc_final: 0.6955 (mmm160) REVERT: C 183 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7636 (mt-10) REVERT: C 300 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7135 (mtp85) REVERT: C 326 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7459 (ttt-90) REVERT: C 380 MET cc_start: 0.8234 (tmm) cc_final: 0.8028 (tmt) REVERT: D 251 PHE cc_start: 0.8613 (m-10) cc_final: 0.8214 (m-80) REVERT: D 292 ILE cc_start: 0.7558 (pp) cc_final: 0.7219 (pt) REVERT: D 303 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8183 (ptt-90) outliers start: 26 outliers final: 12 residues processed: 122 average time/residue: 1.3947 time to fit residues: 178.6975 Evaluate side-chains 123 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 326 ARG Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 303 ARG Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 325 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 89 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 63 optimal weight: 0.1980 chunk 3 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.114748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.082456 restraints weight = 12016.111| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.46 r_work: 0.3102 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7804 Z= 0.185 Angle : 0.485 6.569 10628 Z= 0.250 Chirality : 0.039 0.117 1276 Planarity : 0.004 0.038 1308 Dihedral : 3.095 10.916 1060 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.85 % Allowed : 21.50 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.09 (0.28), residues: 988 helix: 2.55 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.58 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 232 HIS 0.001 0.000 HIS C 310 PHE 0.010 0.001 PHE D 153 TYR 0.009 0.001 TYR C 155 ARG 0.005 0.000 ARG B 294 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.792 Fit side-chains REVERT: A 154 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7929 (tp30) REVERT: A 292 ILE cc_start: 0.6937 (pp) cc_final: 0.6424 (pt) REVERT: A 294 ARG cc_start: 0.6126 (mtm180) cc_final: 0.5780 (mmt90) REVERT: A 326 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7477 (ttt-90) REVERT: A 357 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7442 (mt0) REVERT: B 154 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7742 (tp30) REVERT: B 300 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7214 (mtp85) REVERT: C 154 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7700 (tp30) REVERT: C 163 ARG cc_start: 0.7209 (mtp85) cc_final: 0.6955 (mmm160) REVERT: C 183 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7630 (mt-10) REVERT: C 300 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7131 (mtp85) REVERT: C 326 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7434 (ttt-90) REVERT: C 380 MET cc_start: 0.8246 (tmm) cc_final: 0.8042 (tmt) REVERT: D 251 PHE cc_start: 0.8608 (m-10) cc_final: 0.8207 (m-80) REVERT: D 292 ILE cc_start: 0.7561 (pp) cc_final: 0.7200 (pt) REVERT: D 303 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8180 (ptt-90) outliers start: 22 outliers final: 12 residues processed: 120 average time/residue: 1.4183 time to fit residues: 178.6301 Evaluate side-chains 122 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 326 ARG Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 303 ARG Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 325 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 80 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 96 optimal weight: 0.0970 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.115203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.082905 restraints weight = 11978.800| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.47 r_work: 0.3101 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7804 Z= 0.184 Angle : 0.481 6.530 10628 Z= 0.248 Chirality : 0.039 0.118 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.079 10.740 1060 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.85 % Allowed : 21.63 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.15 (0.28), residues: 988 helix: 2.58 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.65 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 232 HIS 0.001 0.000 HIS C 310 PHE 0.011 0.001 PHE D 153 TYR 0.012 0.001 TYR D 155 ARG 0.006 0.000 ARG B 294 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6887.69 seconds wall clock time: 121 minutes 58.21 seconds (7318.21 seconds total)