Starting phenix.real_space_refine on Thu Jul 2 07:34:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vch_43136/07_2026/8vch_43136.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vch_43136/07_2026/8vch_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 { model { file = "/net/cci-nas-00/data/ceres_data/8vch_43136/07_2026/8vch_43136.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vch_43136/07_2026/8vch_43136.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vch_43136/07_2026/8vch_43136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vch_43136/07_2026/8vch_43136.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Time building chain proxies: 2.00, per 1000 atoms: 0.26 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: 0.58 Conformation dependent library (CDL) restraints added in 465.6 milliseconds 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: 0.20 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: 0.77 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.770 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.600 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:8.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 are 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/Z covalent geometry : bond 0.00358 / 0.16 ( 7804) covalent geometry : angle 0.57778 / 0.33 (10628) hydrogen bonds : bond 0.15480 / 10.56 ( 559) hydrogen bonds : angle 5.02597 / 3.68 ( 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 : 0.370 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: 0.6034 time to fit residues: 70.0065 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 : 0.270 ------------------------------------------------------------------------------- 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: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.115974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.082867 restraints weight = 11950.794| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.54 r_work: 0.3100 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7804 Z= 0.134 Angle : 0.498 5.266 10628 Z= 0.262 Chirality : 0.040 0.126 1276 Planarity : 0.005 0.040 1308 Dihedral : 3.577 34.504 1065 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.72 % Allowed : 16.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.29), residues: 988 helix: 2.29 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.30 (0.44), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 294 TYR 0.009 0.001 TYR D 347 PHE 0.016 0.001 PHE D 336 TRP 0.004 0.001 TRP A 232 HIS 0.002 0.001 HIS B 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.13 ( 7804) covalent geometry : angle 0.49811 / 0.26 (10628) hydrogen bonds : bond 0.03712 / 2.43 ( 559) hydrogen bonds : angle 3.65000 / 2.62 ( 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 : 0.232 Fit side-chains REVERT: A 357 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7736 (mt0) REVERT: A 372 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8894 (mtm) REVERT: C 163 ARG cc_start: 0.7123 (mtp85) cc_final: 0.6901 (mtp85) REVERT: C 183 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7574 (mt-10) REVERT: D 292 ILE cc_start: 0.7494 (pp) cc_final: 0.7099 (pt) outliers start: 21 outliers final: 5 residues processed: 115 average time/residue: 0.5799 time to fit residues: 70.3523 Evaluate side-chains 105 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 372 MET 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: 0.9990 chunk 29 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 52 optimal weight: 0.0670 chunk 95 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.115791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.082902 restraints weight = 11892.640| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.50 r_work: 0.3107 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7804 Z= 0.123 Angle : 0.478 5.227 10628 Z= 0.250 Chirality : 0.039 0.121 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.196 10.498 1060 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.11 % Allowed : 19.04 % 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 are not related in a simple way. whole: 2.83 (0.28), residues: 988 helix: 2.43 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.23 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 294 TYR 0.008 0.001 TYR B 266 PHE 0.015 0.001 PHE D 336 TRP 0.004 0.001 TRP A 232 HIS 0.001 0.000 HIS B 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.12 ( 7804) covalent geometry : angle 0.47805 / 0.25 (10628) hydrogen bonds : bond 0.03306 / 2.15 ( 559) hydrogen bonds : angle 3.47621 / 2.50 ( 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 127 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.201 Fit side-chains REVERT: A 154 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7854 (tp30) REVERT: A 292 ILE cc_start: 0.7258 (pp) cc_final: 0.7058 (pp) REVERT: A 357 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7730 (mt0) REVERT: C 163 ARG cc_start: 0.7236 (mtp85) cc_final: 0.7018 (mtp85) REVERT: C 183 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7685 (mt-10) REVERT: C 300 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7006 (mtp85) REVERT: C 372 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8912 (mtm) REVERT: D 292 ILE cc_start: 0.7648 (pp) cc_final: 0.7270 (pt) outliers start: 24 outliers final: 6 residues processed: 121 average time/residue: 0.5373 time to fit residues: 68.4522 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 : 0.283 ------------------------------------------------------------------------------- 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 372 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: 0.8980 chunk 90 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 78 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.115295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.082083 restraints weight = 12019.243| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.53 r_work: 0.3097 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7804 Z= 0.133 Angle : 0.482 5.263 10628 Z= 0.251 Chirality : 0.040 0.121 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.200 11.043 1060 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.50 % Allowed : 19.56 % Favored : 76.94 % 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 are not related in a simple way. whole: 2.83 (0.28), residues: 988 helix: 2.44 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.19 (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 0.014 0.001 PHE C 336 TRP 0.004 0.001 TRP A 232 HIS 0.001 0.001 HIS B 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.13 ( 7804) covalent geometry : angle 0.48231 / 0.25 (10628) hydrogen bonds : bond 0.03205 / 2.08 ( 559) hydrogen bonds : angle 3.43388 / 2.47 ( 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 131 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.196 Fit side-chains REVERT: A 154 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7637 (tp30) REVERT: A 357 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7589 (mt0) REVERT: B 300 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.6840 (mtp85) REVERT: B 322 LYS cc_start: 0.7402 (mttp) cc_final: 0.7178 (mptt) REVERT: C 163 ARG cc_start: 0.7093 (mtp85) cc_final: 0.6880 (mtp85) REVERT: C 183 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7467 (mt-10) REVERT: C 300 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.6880 (mtp85) REVERT: D 292 ILE cc_start: 0.7629 (pp) cc_final: 0.7229 (pt) outliers start: 27 outliers final: 7 residues processed: 120 average time/residue: 0.5018 time to fit residues: 63.6145 Evaluate side-chains 113 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 4.9990 chunk 7 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 55 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 319 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.114886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.081805 restraints weight = 12014.497| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.51 r_work: 0.3091 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7804 Z= 0.138 Angle : 0.481 5.276 10628 Z= 0.252 Chirality : 0.040 0.120 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.183 11.041 1060 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.40 % Allowed : 18.65 % Favored : 76.94 % 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 are not related in a simple way. whole: 2.81 (0.28), residues: 988 helix: 2.40 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.28 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 294 TYR 0.011 0.001 TYR D 155 PHE 0.013 0.001 PHE C 336 TRP 0.005 0.001 TRP B 150 HIS 0.001 0.001 HIS C 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 7804) covalent geometry : angle 0.48092 / 0.25 (10628) hydrogen bonds : bond 0.03195 / 2.07 ( 559) hydrogen bonds : angle 3.42303 / 2.46 ( 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 138 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.213 Fit side-chains REVERT: A 154 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7817 (tp30) REVERT: A 246 SER cc_start: 0.8221 (OUTLIER) cc_final: 0.7837 (m) REVERT: A 326 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7643 (ttt-90) REVERT: A 357 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7662 (mt0) REVERT: B 154 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7752 (tp30) REVERT: B 300 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7122 (mtp85) REVERT: B 380 MET cc_start: 0.8263 (tmm) cc_final: 0.8006 (tmt) REVERT: C 163 ARG cc_start: 0.7228 (mtp85) cc_final: 0.6933 (mmm160) REVERT: C 183 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7688 (mt-10) REVERT: C 300 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.6890 (mtp85) REVERT: D 292 ILE cc_start: 0.7655 (pp) cc_final: 0.7281 (pt) outliers start: 34 outliers final: 9 residues processed: 127 average time/residue: 0.4969 time to fit residues: 66.6260 Evaluate side-chains 118 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 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 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: 7.9990 chunk 3 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.114418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.081619 restraints weight = 11981.475| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.49 r_work: 0.3093 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7804 Z= 0.141 Angle : 0.497 8.503 10628 Z= 0.257 Chirality : 0.040 0.122 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.186 10.987 1060 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.02 % Allowed : 19.69 % Favored : 76.30 % 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 are not related in a simple way. whole: 2.79 (0.28), residues: 988 helix: 2.38 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.31 (0.44), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 294 TYR 0.009 0.001 TYR C 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/Z covalent geometry : bond 0.00350 / 0.14 ( 7804) covalent geometry : angle 0.49714 / 0.26 (10628) hydrogen bonds : bond 0.03167 / 2.05 ( 559) hydrogen bonds : angle 3.40696 / 2.46 ( 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 140 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.233 Fit side-chains REVERT: A 154 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7871 (tp30) REVERT: A 326 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7596 (ttt-90) REVERT: A 357 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7608 (mt0) REVERT: B 154 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7765 (tp30) REVERT: B 300 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7081 (mtp85) REVERT: C 154 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7683 (tp30) REVERT: C 163 ARG cc_start: 0.7220 (mtp85) cc_final: 0.6928 (mmm160) REVERT: C 183 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7632 (mt-10) REVERT: C 300 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7024 (mtp85) REVERT: D 292 ILE cc_start: 0.7547 (pp) cc_final: 0.7189 (pt) REVERT: D 380 MET cc_start: 0.8220 (tmm) cc_final: 0.7998 (tmt) outliers start: 31 outliers final: 13 residues processed: 125 average time/residue: 0.5591 time to fit residues: 73.4236 Evaluate side-chains 122 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 40 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 0.1980 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.114722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.081837 restraints weight = 11978.475| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.49 r_work: 0.3095 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7804 Z= 0.129 Angle : 0.486 7.365 10628 Z= 0.251 Chirality : 0.040 0.124 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.143 11.111 1060 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.24 % Allowed : 20.60 % 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 are not related in a simple way. whole: 2.85 (0.28), residues: 988 helix: 2.41 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.36 (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 D 155 PHE 0.011 0.001 PHE C 336 TRP 0.004 0.001 TRP A 232 HIS 0.001 0.000 HIS C 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 ( 7804) covalent geometry : angle 0.48604 / 0.25 (10628) hydrogen bonds : bond 0.03105 / 2.01 ( 559) hydrogen bonds : angle 3.36793 / 2.43 ( 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 133 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.179 Fit side-chains REVERT: A 154 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7822 (tp30) REVERT: A 294 ARG cc_start: 0.5689 (mtm180) cc_final: 0.5150 (mmt90) REVERT: A 326 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7564 (ttt-90) REVERT: A 357 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7555 (mt0) REVERT: B 154 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7867 (tp30) REVERT: B 300 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7217 (mtp85) REVERT: B 380 MET cc_start: 0.8281 (tmm) cc_final: 0.8031 (tmt) REVERT: C 154 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7732 (tp30) REVERT: C 183 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7693 (mt-10) REVERT: C 300 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7140 (mtp85) REVERT: C 326 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7509 (ttt-90) REVERT: D 251 PHE cc_start: 0.8625 (m-10) cc_final: 0.8233 (m-80) REVERT: D 292 ILE cc_start: 0.7548 (pp) cc_final: 0.7195 (pt) REVERT: D 380 MET cc_start: 0.8230 (tmm) cc_final: 0.8024 (tmt) outliers start: 25 outliers final: 10 residues processed: 123 average time/residue: 0.5466 time to fit residues: 70.4007 Evaluate side-chains 122 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 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 300 ARG Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 326 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 0.0970 chunk 63 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 41 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.114704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.082301 restraints weight = 12067.180| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.48 r_work: 0.3102 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 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 0.039 7804 Z= 0.117 Angle : 0.485 7.426 10628 Z= 0.251 Chirality : 0.039 0.119 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.118 10.955 1060 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.98 % Allowed : 21.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.92 (0.28), residues: 988 helix: 2.47 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.37 (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 C 155 PHE 0.010 0.001 PHE C 336 TRP 0.005 0.001 TRP A 232 HIS 0.001 0.000 HIS B 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 7804) covalent geometry : angle 0.48504 / 0.25 (10628) hydrogen bonds : bond 0.03010 / 1.95 ( 559) hydrogen bonds : angle 3.33658 / 2.41 ( 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 131 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.299 Fit side-chains REVERT: A 154 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7781 (tp30) REVERT: A 292 ILE cc_start: 0.7139 (pp) cc_final: 0.6509 (pt) REVERT: A 294 ARG cc_start: 0.5708 (mtm180) cc_final: 0.5383 (mmt90) REVERT: A 357 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7449 (mt0) REVERT: B 154 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7799 (tp30) REVERT: B 300 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7225 (mtp85) REVERT: C 154 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7795 (tp30) REVERT: C 183 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7676 (mt-10) REVERT: C 300 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7289 (mtp85) REVERT: C 326 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7509 (ttt-90) REVERT: D 251 PHE cc_start: 0.8624 (m-10) cc_final: 0.8305 (m-80) REVERT: D 292 ILE cc_start: 0.7553 (pp) cc_final: 0.7207 (pt) REVERT: D 380 MET cc_start: 0.8249 (tmm) cc_final: 0.7989 (tmt) outliers start: 23 outliers final: 10 residues processed: 119 average time/residue: 0.5860 time to fit residues: 73.2837 Evaluate side-chains 118 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 372 MET Chi-restraints excluded: chain C residue 419 ARG 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 90 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 59 optimal weight: 0.0170 chunk 58 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.114582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.082007 restraints weight = 12018.573| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.48 r_work: 0.3098 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1852 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= 0.128 Angle : 0.489 7.153 10628 Z= 0.253 Chirality : 0.039 0.118 1276 Planarity : 0.004 0.043 1308 Dihedral : 3.130 10.916 1060 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.91 (0.28), residues: 988 helix: 2.44 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.41 (0.44), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 294 TYR 0.010 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/Z covalent geometry : bond 0.00318 / 0.13 ( 7804) covalent geometry : angle 0.48879 / 0.25 (10628) hydrogen bonds : bond 0.03060 / 1.98 ( 559) hydrogen bonds : angle 3.34282 / 2.42 ( 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 128 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.186 Fit side-chains REVERT: A 154 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7769 (tp30) REVERT: A 292 ILE cc_start: 0.7157 (pp) cc_final: 0.6519 (pt) REVERT: A 294 ARG cc_start: 0.6106 (mtm180) cc_final: 0.5716 (mmt90) REVERT: A 326 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7537 (ttt-90) REVERT: A 357 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7455 (mt0) REVERT: B 154 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7837 (tp30) REVERT: B 300 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7199 (mtp85) REVERT: C 154 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7837 (tp30) REVERT: C 183 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7680 (mt-10) REVERT: C 300 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7146 (mtp85) REVERT: C 326 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7509 (ttt-90) REVERT: D 251 PHE cc_start: 0.8621 (m-10) cc_final: 0.8304 (m-80) REVERT: D 292 ILE cc_start: 0.7551 (pp) cc_final: 0.7209 (pt) REVERT: D 380 MET cc_start: 0.8246 (tmm) cc_final: 0.7982 (tmt) outliers start: 22 outliers final: 14 residues processed: 120 average time/residue: 0.5634 time to fit residues: 71.0959 Evaluate side-chains 126 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 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 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 335 LEU Chi-restraints excluded: chain C residue 419 ARG 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: 0.9990 chunk 77 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 0.0770 chunk 86 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.115020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.082472 restraints weight = 12022.784| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.49 r_work: 0.3099 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1903 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= 0.117 Angle : 0.476 7.119 10628 Z= 0.246 Chirality : 0.039 0.119 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.106 10.896 1060 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.85 % Allowed : 21.76 % Favored : 75.39 % 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 are not related in a simple way. whole: 2.98 (0.28), residues: 988 helix: 2.48 (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 A 155 PHE 0.010 0.001 PHE B 336 TRP 0.005 0.001 TRP A 232 HIS 0.001 0.000 HIS C 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 7804) covalent geometry : angle 0.47638 / 0.25 (10628) hydrogen bonds : bond 0.03005 / 1.95 ( 559) hydrogen bonds : angle 3.30392 / 2.39 ( 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 127 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.304 Fit side-chains REVERT: A 154 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7913 (tp30) REVERT: A 292 ILE cc_start: 0.7176 (pp) cc_final: 0.6543 (pt) REVERT: A 294 ARG cc_start: 0.5964 (mtm180) cc_final: 0.5557 (mmt90) REVERT: A 326 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7462 (ttt-90) REVERT: A 357 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7437 (mt0) REVERT: B 154 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7818 (tp30) REVERT: B 300 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7230 (mtp85) REVERT: C 154 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7833 (tp30) REVERT: C 183 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7643 (mt-10) REVERT: C 226 GLU cc_start: 0.8367 (tp30) cc_final: 0.8142 (tp30) REVERT: C 300 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.7154 (mtp85) REVERT: C 326 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7498 (ttt-90) REVERT: D 251 PHE cc_start: 0.8622 (m-10) cc_final: 0.8296 (m-80) REVERT: D 292 ILE cc_start: 0.7559 (pp) cc_final: 0.7197 (pt) REVERT: D 380 MET cc_start: 0.8248 (tmm) cc_final: 0.7993 (tmt) outliers start: 22 outliers final: 12 residues processed: 117 average time/residue: 0.5490 time to fit residues: 67.6116 Evaluate side-chains 121 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 157 GLU 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 C residue 326 ARG Chi-restraints excluded: chain C residue 372 MET 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: 0.6980 chunk 48 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 96 optimal weight: 0.1980 chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 414 ASN C 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.115330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.082934 restraints weight = 12064.336| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.46 r_work: 0.3110 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7804 Z= 0.108 Angle : 0.470 7.087 10628 Z= 0.243 Chirality : 0.039 0.117 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.057 10.764 1060 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.85 % Allowed : 21.76 % Favored : 75.39 % 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 are not related in a simple way. whole: 3.10 (0.28), residues: 988 helix: 2.55 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.59 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 294 TYR 0.013 0.001 TYR D 155 PHE 0.010 0.001 PHE C 336 TRP 0.006 0.001 TRP A 232 HIS 0.001 0.000 HIS C 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 7804) covalent geometry : angle 0.47015 / 0.24 (10628) hydrogen bonds : bond 0.02938 / 1.90 ( 559) hydrogen bonds : angle 3.27682 / 2.37 ( 1587) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2794.24 seconds wall clock time: 48 minutes 7.55 seconds (2887.55 seconds total)