Starting phenix.real_space_refine on Wed Sep 17 09:19:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vch_43136/09_2025/8vch_43136.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vch_43136/09_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_43136/09_2025/8vch_43136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vch_43136/09_2025/8vch_43136.map" model { file = "/net/cci-nas-00/data/ceres_data/8vch_43136/09_2025/8vch_43136.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vch_43136/09_2025/8vch_43136.cif" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 3, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 5, 'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} 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: {'ARG:plan': 3, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 5, 'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} 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: {'ARG:plan': 3, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 5, 'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} 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: {'ARG:plan': 3, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 5, 'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} 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: 2.16, per 1000 atoms: 0.28 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: 0.68 Conformation dependent library (CDL) restraints added in 389.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.24 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: 1.18 Time building geometry restraints manager: 0.88 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: 0.01 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.090 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 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:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.500 ------------------------------------------------------------------------------- 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= 0.155 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.005 0.001 ARG B 294 TYR 0.012 0.002 TYR A 155 PHE 0.016 0.001 PHE B 153 TRP 0.006 0.001 TRP A 150 HIS 0.002 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 7804) covalent geometry : angle 0.57778 (10628) hydrogen bonds : bond 0.15480 ( 559) hydrogen bonds : angle 5.02597 ( 1587) *********************** 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 : 0.305 Fit side-chains REVERT: B 260 ILE cc_start: 0.7782 (mt) cc_final: 0.7504 (mp) outliers start: 6 outliers final: 2 residues processed: 110 average time/residue: 0.6641 time to fit residues: 76.7720 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 : 0.337 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 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 = 0.3730 r_free = 0.3730 target = 0.116188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.083276 restraints weight = 11865.362| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.50 r_work: 0.3108 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.0938 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= 0.128 Angle : 0.494 5.241 10628 Z= 0.260 Chirality : 0.040 0.126 1276 Planarity : 0.005 0.040 1308 Dihedral : 3.531 34.259 1065 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.72 % Allowed : 16.32 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.75 (0.28), residues: 988 helix: 2.33 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.34 (0.44), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 294 TYR 0.009 0.001 TYR D 347 PHE 0.015 0.001 PHE D 336 TRP 0.003 0.001 TRP A 232 HIS 0.002 0.001 HIS B 310 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 7804) covalent geometry : angle 0.49414 (10628) hydrogen bonds : bond 0.03651 ( 559) hydrogen bonds : angle 3.63607 ( 1587) *********************** 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 121 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.316 Fit side-chains REVERT: A 352 ASP cc_start: 0.8474 (m-30) cc_final: 0.8256 (m-30) REVERT: A 357 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7750 (mt0) REVERT: C 163 ARG cc_start: 0.7224 (mtp85) cc_final: 0.6999 (mtp85) REVERT: C 183 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7783 (mt-10) REVERT: D 292 ILE cc_start: 0.7534 (pp) cc_final: 0.7146 (pt) outliers start: 21 outliers final: 5 residues processed: 115 average time/residue: 0.6570 time to fit residues: 79.4976 Evaluate side-chains 104 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 44 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.115805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.082798 restraints weight = 11930.830| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.52 r_work: 0.3100 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7804 Z= 0.134 Angle : 0.485 5.252 10628 Z= 0.253 Chirality : 0.040 0.121 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.191 10.313 1060 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.98 % Allowed : 19.17 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.86 (0.28), residues: 988 helix: 2.44 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.29 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 294 TYR 0.009 0.001 TYR B 266 PHE 0.015 0.001 PHE B 336 TRP 0.004 0.001 TRP A 232 HIS 0.002 0.001 HIS B 310 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 7804) covalent geometry : angle 0.48501 (10628) hydrogen bonds : bond 0.03371 ( 559) hydrogen bonds : angle 3.48381 ( 1587) *********************** 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 128 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.313 Fit side-chains REVERT: A 154 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7853 (tp30) REVERT: A 292 ILE cc_start: 0.7221 (pp) cc_final: 0.7018 (pp) REVERT: A 357 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7726 (mt0) REVERT: C 163 ARG cc_start: 0.7220 (mtp85) cc_final: 0.6999 (mtp85) REVERT: C 183 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7657 (mt-10) REVERT: C 300 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7016 (mtp85) REVERT: D 292 ILE cc_start: 0.7642 (pp) cc_final: 0.7249 (pt) outliers start: 23 outliers final: 7 residues processed: 122 average time/residue: 0.6918 time to fit residues: 88.5922 Evaluate side-chains 111 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 325 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.115378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.082450 restraints weight = 11971.348| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.49 r_work: 0.3098 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7804 Z= 0.134 Angle : 0.483 5.256 10628 Z= 0.251 Chirality : 0.040 0.121 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.196 11.179 1060 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.86 (0.28), residues: 988 helix: 2.45 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.26 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 294 TYR 0.010 0.001 TYR B 266 PHE 0.013 0.001 PHE B 336 TRP 0.004 0.001 TRP A 232 HIS 0.001 0.001 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 7804) covalent geometry : angle 0.48309 (10628) hydrogen bonds : bond 0.03227 ( 559) hydrogen bonds : angle 3.44040 ( 1587) *********************** 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 130 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.316 Fit side-chains REVERT: A 154 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7757 (tp30) REVERT: A 246 SER cc_start: 0.8222 (OUTLIER) cc_final: 0.7775 (m) REVERT: A 292 ILE cc_start: 0.7181 (pp) cc_final: 0.6978 (pp) REVERT: A 357 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7559 (mt0) REVERT: B 300 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7126 (mtp85) REVERT: B 322 LYS cc_start: 0.7521 (mttp) cc_final: 0.7298 (mptt) REVERT: C 163 ARG cc_start: 0.7193 (mtp85) cc_final: 0.6893 (mmm160) REVERT: C 183 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7682 (mt-10) REVERT: C 300 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.6935 (mtp85) REVERT: D 292 ILE cc_start: 0.7656 (pp) cc_final: 0.7267 (pt) outliers start: 25 outliers final: 8 residues processed: 122 average time/residue: 0.6601 time to fit residues: 84.6189 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 : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 325 MET 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 54 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 55 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.114948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.081995 restraints weight = 11970.920| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.48 r_work: 0.3092 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7804 Z= 0.135 Angle : 0.486 8.501 10628 Z= 0.250 Chirality : 0.040 0.120 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.169 11.025 1060 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.50 % Allowed : 19.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.88 (0.28), residues: 988 helix: 2.45 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.33 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 294 TYR 0.012 0.001 TYR B 266 PHE 0.013 0.001 PHE B 336 TRP 0.004 0.001 TRP A 232 HIS 0.001 0.001 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 7804) covalent geometry : angle 0.48637 (10628) hydrogen bonds : bond 0.03194 ( 559) hydrogen bonds : angle 3.38701 ( 1587) *********************** 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 134 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.242 Fit side-chains REVERT: A 154 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7780 (tp30) REVERT: A 326 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7571 (ttt-90) REVERT: A 357 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7665 (mt0) REVERT: B 260 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.8012 (mt) REVERT: B 300 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7098 (mtp85) REVERT: C 163 ARG cc_start: 0.7195 (mtp85) cc_final: 0.6903 (mmm160) REVERT: C 183 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7683 (mt-10) REVERT: C 300 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.7027 (mtp85) REVERT: D 292 ILE cc_start: 0.7694 (pp) cc_final: 0.7330 (pt) REVERT: D 380 MET cc_start: 0.8225 (tmm) cc_final: 0.8020 (tmt) outliers start: 27 outliers final: 11 residues processed: 123 average time/residue: 0.6556 time to fit residues: 84.7139 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 : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 325 MET 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 B residue 325 MET Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 325 MET 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 80 optimal weight: 9.9990 chunk 3 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.114585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.081825 restraints weight = 11938.525| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.47 r_work: 0.3090 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1661 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= 0.134 Angle : 0.489 6.890 10628 Z= 0.252 Chirality : 0.040 0.119 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.166 11.200 1060 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.63 % Allowed : 19.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.87 (0.28), residues: 988 helix: 2.42 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.38 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 294 TYR 0.010 0.001 TYR B 155 PHE 0.012 0.001 PHE B 336 TRP 0.004 0.001 TRP A 232 HIS 0.001 0.000 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 7804) covalent geometry : angle 0.48947 (10628) hydrogen bonds : bond 0.03159 ( 559) hydrogen bonds : angle 3.38285 ( 1587) *********************** 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: 28 poor density : 110 time to evaluate : 0.227 Fit side-chains REVERT: A 154 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7836 (tp30) REVERT: A 294 ARG cc_start: 0.5719 (mtm180) cc_final: 0.5168 (mmt90) REVERT: A 326 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7555 (ttt-90) REVERT: A 357 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7574 (mt0) REVERT: B 260 ILE cc_start: 0.8237 (mt) cc_final: 0.7998 (mt) REVERT: B 300 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7194 (mtp85) REVERT: C 154 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7711 (tp30) REVERT: C 163 ARG cc_start: 0.7196 (mtp85) cc_final: 0.6912 (mmm160) REVERT: C 183 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7684 (mt-10) REVERT: C 300 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7136 (mtp85) REVERT: D 292 ILE cc_start: 0.7541 (pp) cc_final: 0.7181 (pt) outliers start: 28 outliers final: 13 residues processed: 124 average time/residue: 0.6791 time to fit residues: 88.1733 Evaluate side-chains 123 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 325 MET 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 261 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 325 MET 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 90 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.114472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.081812 restraints weight = 11907.629| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.45 r_work: 0.3090 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1716 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= 0.134 Angle : 0.490 6.857 10628 Z= 0.252 Chirality : 0.040 0.120 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.156 11.122 1060 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.76 % Allowed : 20.08 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.90 (0.28), residues: 988 helix: 2.44 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.40 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 294 TYR 0.011 0.001 TYR D 155 PHE 0.011 0.001 PHE B 336 TRP 0.004 0.001 TRP A 232 HIS 0.001 0.000 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 7804) covalent geometry : angle 0.48996 (10628) hydrogen bonds : bond 0.03150 ( 559) hydrogen bonds : angle 3.35722 ( 1587) *********************** 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 137 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.315 Fit side-chains REVERT: A 154 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7807 (tp30) REVERT: A 326 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7521 (ttt-90) REVERT: A 357 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7531 (mt0) REVERT: B 260 ILE cc_start: 0.8183 (mt) cc_final: 0.7956 (mt) REVERT: B 300 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7204 (mtp85) REVERT: C 154 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7772 (tp30) REVERT: C 183 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7597 (mt-10) REVERT: C 300 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.7123 (mtp85) REVERT: D 251 PHE cc_start: 0.8629 (m-10) cc_final: 0.8246 (m-80) REVERT: D 292 ILE cc_start: 0.7545 (pp) cc_final: 0.7192 (pt) outliers start: 29 outliers final: 14 residues processed: 126 average time/residue: 0.7001 time to fit residues: 92.4807 Evaluate side-chains 125 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 325 MET 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 408 VAL 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 B residue 325 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 408 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 15 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.114420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.081958 restraints weight = 12071.883| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.47 r_work: 0.3091 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7804 Z= 0.125 Angle : 0.492 6.585 10628 Z= 0.254 Chirality : 0.040 0.119 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.135 11.222 1060 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.76 % Allowed : 20.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.97 (0.28), residues: 988 helix: 2.49 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.43 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 294 TYR 0.011 0.001 TYR C 155 PHE 0.011 0.001 PHE B 336 TRP 0.005 0.001 TRP A 232 HIS 0.001 0.000 HIS B 310 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 7804) covalent geometry : angle 0.49181 (10628) hydrogen bonds : bond 0.03090 ( 559) hydrogen bonds : angle 3.33834 ( 1587) *********************** 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 139 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.314 Fit side-chains REVERT: A 154 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7766 (tp30) REVERT: A 292 ILE cc_start: 0.7109 (pp) cc_final: 0.6506 (pt) REVERT: A 294 ARG cc_start: 0.6205 (mtm-85) cc_final: 0.5968 (mmt90) REVERT: A 326 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7497 (ttt-90) REVERT: A 357 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7462 (mt0) REVERT: B 154 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7782 (tp30) REVERT: B 300 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7215 (mtp85) REVERT: C 154 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7680 (tp30) REVERT: C 183 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7673 (mt-10) REVERT: C 300 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7127 (mtp85) REVERT: C 326 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7483 (ttt-90) REVERT: D 251 PHE cc_start: 0.8631 (m-10) cc_final: 0.8300 (m-80) REVERT: D 292 ILE cc_start: 0.7556 (pp) cc_final: 0.7210 (pt) outliers start: 29 outliers final: 16 residues processed: 126 average time/residue: 0.6879 time to fit residues: 90.7679 Evaluate side-chains 128 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 325 MET 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 408 VAL 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 B residue 325 MET Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 326 ARG Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 408 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 90 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.114136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.081647 restraints weight = 11995.276| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.45 r_work: 0.3088 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1829 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= 0.136 Angle : 0.491 6.406 10628 Z= 0.254 Chirality : 0.040 0.120 1276 Planarity : 0.004 0.038 1308 Dihedral : 3.164 11.021 1060 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.50 % Allowed : 20.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.96 (0.28), residues: 988 helix: 2.46 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.50 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 294 TYR 0.010 0.001 TYR D 155 PHE 0.012 0.001 PHE D 336 TRP 0.005 0.001 TRP A 232 HIS 0.001 0.000 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 7804) covalent geometry : angle 0.49142 (10628) hydrogen bonds : bond 0.03151 ( 559) hydrogen bonds : angle 3.34178 ( 1587) *********************** 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: 27 poor density : 106 time to evaluate : 0.292 Fit side-chains REVERT: A 154 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7825 (tp30) REVERT: A 273 GLU cc_start: 0.7539 (tp30) cc_final: 0.7234 (tm-30) REVERT: A 292 ILE cc_start: 0.7159 (pp) cc_final: 0.6533 (pt) REVERT: A 294 ARG cc_start: 0.6122 (mtm-85) cc_final: 0.5891 (mmt90) REVERT: A 326 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7489 (ttt-90) REVERT: A 357 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7441 (mt0) REVERT: B 154 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7864 (tp30) REVERT: B 300 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7212 (mtp85) REVERT: C 154 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7740 (tp30) REVERT: C 183 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7667 (mt-10) REVERT: C 300 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.6985 (mtp85) REVERT: C 326 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7469 (ttt-90) REVERT: D 251 PHE cc_start: 0.8631 (m-10) cc_final: 0.8315 (m-80) REVERT: D 292 ILE cc_start: 0.7538 (pp) cc_final: 0.7168 (pt) outliers start: 27 outliers final: 19 residues processed: 121 average time/residue: 0.6896 time to fit residues: 87.5920 Evaluate side-chains 130 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 325 MET 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 260 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 326 ARG Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 408 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 51 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 79 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.114577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.081977 restraints weight = 11925.467| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.46 r_work: 0.3093 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7804 Z= 0.122 Angle : 0.491 6.461 10628 Z= 0.253 Chirality : 0.039 0.118 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.139 11.017 1060 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.37 % Allowed : 20.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.01 (0.28), residues: 988 helix: 2.50 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.51 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 294 TYR 0.009 0.001 TYR C 155 PHE 0.010 0.001 PHE B 336 TRP 0.006 0.001 TRP A 232 HIS 0.001 0.000 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7804) covalent geometry : angle 0.49063 (10628) hydrogen bonds : bond 0.03091 ( 559) hydrogen bonds : angle 3.33563 ( 1587) ********************** 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 132 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.304 Fit side-chains REVERT: A 154 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7757 (tp30) REVERT: A 292 ILE cc_start: 0.7174 (pp) cc_final: 0.6554 (pt) REVERT: A 294 ARG cc_start: 0.6048 (mtm-85) cc_final: 0.5780 (mmt90) REVERT: A 326 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7475 (ttt-90) REVERT: A 357 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7408 (mt0) REVERT: B 154 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7814 (tp30) REVERT: B 300 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7211 (mtp85) REVERT: C 154 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7821 (tp30) REVERT: C 183 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7636 (mt-10) REVERT: C 300 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7110 (mtp85) REVERT: C 326 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7455 (ttt-90) REVERT: D 251 PHE cc_start: 0.8632 (m-10) cc_final: 0.8315 (m-80) REVERT: D 292 ILE cc_start: 0.7547 (pp) cc_final: 0.7182 (pt) outliers start: 26 outliers final: 11 residues processed: 119 average time/residue: 0.6989 time to fit residues: 87.2986 Evaluate side-chains 121 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 292 ILE Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 326 ARG Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain D residue 298 LEU 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 17 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 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 = 0.3711 r_free = 0.3711 target = 0.114014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.081806 restraints weight = 11974.901| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.43 r_work: 0.3087 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7804 Z= 0.132 Angle : 0.490 6.316 10628 Z= 0.253 Chirality : 0.040 0.119 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.150 10.994 1060 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.72 % Allowed : 21.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.99 (0.28), residues: 988 helix: 2.48 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.54 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 294 TYR 0.010 0.001 TYR D 155 PHE 0.012 0.001 PHE D 336 TRP 0.005 0.001 TRP A 232 HIS 0.001 0.000 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 7804) covalent geometry : angle 0.48960 (10628) hydrogen bonds : bond 0.03118 ( 559) hydrogen bonds : angle 3.31718 ( 1587) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3679.30 seconds wall clock time: 63 minutes 16.19 seconds (3796.19 seconds total)