Starting phenix.real_space_refine on Mon Apr 28 13:33:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vch_43136/04_2025/8vch_43136.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vch_43136/04_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_43136/04_2025/8vch_43136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vch_43136/04_2025/8vch_43136.map" model { file = "/net/cci-nas-00/data/ceres_data/8vch_43136/04_2025/8vch_43136.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vch_43136/04_2025/8vch_43136.cif" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 32 5.16 5 C 5104 2.51 5 N 1192 2.21 5 O 1284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7614 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1903 Classifications: {'peptide': 253} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 239} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1903 Classifications: {'peptide': 253} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 239} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "C" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1903 Classifications: {'peptide': 253} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 239} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "D" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1903 Classifications: {'peptide': 253} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 239} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.51, per 1000 atoms: 0.72 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: 2.09 Conformation dependent library (CDL) restraints added in 1.2 seconds 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1864 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 145 through 155 Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 159 through 184 removed outlier: 4.195A pdb=" N THR A 184 " --> pdb=" O PHE A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 244 Processing helix chain 'A' and resid 249 through 252 Processing helix chain 'A' and resid 253 through 262 removed outlier: 3.729A pdb=" N ASP A 259 " --> pdb=" O MET A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 275 removed outlier: 3.680A pdb=" N PHE A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 300 Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 311 through 324 Processing helix chain 'A' and resid 324 through 350 Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 373 Processing helix chain 'A' and resid 384 through 403 removed outlier: 3.642A pdb=" N VAL A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.669A pdb=" N ILE A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 159 through 184 removed outlier: 4.125A pdb=" N THR B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 244 Processing helix chain 'B' and resid 253 through 262 removed outlier: 3.872A pdb=" N ASP B 259 " --> pdb=" O MET B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 275 removed outlier: 3.620A pdb=" N PHE B 267 " --> pdb=" O ILE B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 300 removed outlier: 3.560A pdb=" N ARG B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 310 Processing helix chain 'B' and resid 311 through 324 Processing helix chain 'B' and resid 324 through 350 Processing helix chain 'B' and resid 361 through 363 No H-bonds generated for 'chain 'B' and resid 361 through 363' Processing helix chain 'B' and resid 364 through 373 Processing helix chain 'B' and resid 384 through 403 removed outlier: 3.660A pdb=" N VAL B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 419 removed outlier: 3.651A pdb=" N ILE B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 155 Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 159 through 184 removed outlier: 3.610A pdb=" N ARG C 163 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR C 184 " --> pdb=" O PHE C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 244 Processing helix chain 'C' and resid 249 through 252 Processing helix chain 'C' and resid 253 through 262 removed outlier: 3.700A pdb=" N ASP C 259 " --> pdb=" O MET C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 275 removed outlier: 3.605A pdb=" N PHE C 267 " --> pdb=" O ILE C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 300 removed outlier: 3.534A pdb=" N ARG C 300 " --> pdb=" O ILE C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 310 Processing helix chain 'C' and resid 311 through 324 Processing helix chain 'C' and resid 324 through 350 Processing helix chain 'C' and resid 361 through 363 No H-bonds generated for 'chain 'C' and resid 361 through 363' Processing helix chain 'C' and resid 364 through 373 Processing helix chain 'C' and resid 384 through 403 removed outlier: 3.661A pdb=" N VAL C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 419 removed outlier: 3.698A pdb=" N ILE C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 156 through 158 No H-bonds generated for 'chain 'D' and resid 156 through 158' Processing helix chain 'D' and resid 159 through 184 removed outlier: 4.154A pdb=" N THR D 184 " --> pdb=" O PHE D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 244 Processing helix chain 'D' and resid 253 through 262 removed outlier: 3.732A pdb=" N ASP D 259 " --> pdb=" O MET D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 275 removed outlier: 3.649A pdb=" N PHE D 267 " --> pdb=" O ILE D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 300 Processing helix chain 'D' and resid 301 through 310 Processing helix chain 'D' and resid 311 through 324 Processing helix chain 'D' and resid 324 through 350 Processing helix chain 'D' and resid 361 through 363 No H-bonds generated for 'chain 'D' and resid 361 through 363' Processing helix chain 'D' and resid 364 through 373 Processing helix chain 'D' and resid 384 through 403 removed outlier: 3.614A pdb=" N VAL D 399 " --> pdb=" O ALA D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 419 removed outlier: 3.518A pdb=" N ILE D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) 559 hydrogen bonds defined for protein. 1587 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2296 1.34 - 1.46: 1835 1.46 - 1.58: 3625 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 7804 Sorted by residual: bond pdb=" CB VAL C 370 " pdb=" CG1 VAL C 370 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.53e+00 bond pdb=" CB VAL A 370 " pdb=" CG1 VAL A 370 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.41e+00 bond pdb=" CB GLU C 273 " pdb=" CG GLU C 273 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.39e+00 bond pdb=" CB VAL D 370 " pdb=" CG1 VAL D 370 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.34e+00 bond pdb=" CB VAL B 370 " pdb=" CG1 VAL B 370 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.33e+00 ... (remaining 7799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 10152 1.16 - 2.33: 363 2.33 - 3.49: 71 3.49 - 4.66: 32 4.66 - 5.82: 10 Bond angle restraints: 10628 Sorted by residual: angle pdb=" N ILE D 263 " pdb=" CA ILE D 263 " pdb=" C ILE D 263 " ideal model delta sigma weight residual 113.42 108.53 4.89 1.17e+00 7.31e-01 1.75e+01 angle pdb=" N ILE B 263 " pdb=" CA ILE B 263 " pdb=" C ILE B 263 " ideal model delta sigma weight residual 113.42 108.70 4.72 1.17e+00 7.31e-01 1.63e+01 angle pdb=" N ILE C 263 " pdb=" CA ILE C 263 " pdb=" C ILE C 263 " ideal model delta sigma weight residual 113.42 108.89 4.53 1.17e+00 7.31e-01 1.50e+01 angle pdb=" N ILE A 263 " pdb=" CA ILE A 263 " pdb=" C ILE A 263 " ideal model delta sigma weight residual 113.42 109.04 4.38 1.17e+00 7.31e-01 1.40e+01 angle pdb=" CA GLU C 273 " pdb=" CB GLU C 273 " pdb=" CG GLU C 273 " ideal model delta sigma weight residual 114.10 119.92 -5.82 2.00e+00 2.50e-01 8.47e+00 ... (remaining 10623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 3885 16.47 - 32.94: 429 32.94 - 49.40: 125 49.40 - 65.87: 15 65.87 - 82.34: 6 Dihedral angle restraints: 4460 sinusoidal: 1572 harmonic: 2888 Sorted by residual: dihedral pdb=" CG ARG B 309 " pdb=" CD ARG B 309 " pdb=" NE ARG B 309 " pdb=" CZ ARG B 309 " ideal model delta sinusoidal sigma weight residual -180.00 -137.90 -42.10 2 1.50e+01 4.44e-03 9.59e+00 dihedral pdb=" CB MET A 372 " pdb=" CG MET A 372 " pdb=" SD MET A 372 " pdb=" CE MET A 372 " ideal model delta sinusoidal sigma weight residual -60.00 -1.12 -58.88 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB MET A 325 " pdb=" CG MET A 325 " pdb=" SD MET A 325 " pdb=" CE MET A 325 " ideal model delta sinusoidal sigma weight residual 180.00 121.72 58.28 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 4457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 589 0.023 - 0.047: 358 0.047 - 0.070: 213 0.070 - 0.094: 78 0.094 - 0.117: 38 Chirality restraints: 1276 Sorted by residual: chirality pdb=" CA PRO A 407 " pdb=" N PRO A 407 " pdb=" C PRO A 407 " pdb=" CB PRO A 407 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.44e-01 chirality pdb=" CA PRO C 407 " pdb=" N PRO C 407 " pdb=" C PRO C 407 " pdb=" CB PRO C 407 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.42e-01 chirality pdb=" CA ASP C 355 " pdb=" N ASP C 355 " pdb=" C ASP C 355 " pdb=" CB ASP C 355 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.39e-01 ... (remaining 1273 not shown) Planarity restraints: 1308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 160 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO A 161 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 160 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO D 161 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 161 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 161 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 160 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO B 161 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 161 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 161 " -0.021 5.00e-02 4.00e+02 ... (remaining 1305 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.84: 2656 2.84 - 3.41: 8585 3.41 - 3.99: 13935 3.99 - 4.56: 20502 4.56 - 5.14: 28010 Nonbonded interactions: 73688 Sorted by model distance: nonbonded pdb=" OD2 ASP A 352 " pdb=" NH2 ARG B 294 " model vdw 2.260 3.120 nonbonded pdb=" OE1 GLU D 353 " pdb=" OG1 THR D 383 " model vdw 2.282 3.040 nonbonded pdb=" OE1 GLU B 353 " pdb=" OG1 THR B 383 " model vdw 2.302 3.040 nonbonded pdb=" OE1 GLU A 353 " pdb=" OG1 THR A 383 " model vdw 2.319 3.040 nonbonded pdb=" OE1 GLU B 183 " pdb=" NH2 ARG B 300 " model vdw 2.390 3.120 ... (remaining 73683 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 138 through 421) selection = chain 'B' selection = (chain 'C' and resid 138 through 421) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.880 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.460 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.27), residues: 988 helix: 2.03 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -0.36 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 150 HIS 0.002 0.001 HIS A 310 PHE 0.016 0.001 PHE B 153 TYR 0.012 0.002 TYR A 155 ARG 0.005 0.001 ARG B 294 Details of bonding type rmsd hydrogen bonds : bond 0.15480 ( 559) hydrogen bonds : angle 5.02597 ( 1587) covalent geometry : bond 0.00358 ( 7804) covalent geometry : angle 0.57778 (10628) *********************** 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 : 0.932 Fit side-chains REVERT: B 260 ILE cc_start: 0.7782 (mt) cc_final: 0.7512 (mp) outliers start: 6 outliers final: 2 residues processed: 110 average time/residue: 1.2853 time to fit residues: 149.2085 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 : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain B residue 419 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 25 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.116648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.082831 restraints weight = 11590.402| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.59 r_work: 0.3108 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7804 Z= 0.147 Angle : 0.505 5.299 10628 Z= 0.266 Chirality : 0.040 0.129 1276 Planarity : 0.005 0.040 1308 Dihedral : 3.571 34.984 1065 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.59 % Allowed : 16.97 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.29), residues: 988 helix: 2.27 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.36 (0.44), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 232 HIS 0.002 0.001 HIS B 310 PHE 0.016 0.001 PHE D 336 TYR 0.009 0.001 TYR D 347 ARG 0.004 0.000 ARG B 294 Details of bonding type rmsd hydrogen bonds : bond 0.03944 ( 559) hydrogen bonds : angle 3.68839 ( 1587) covalent geometry : bond 0.00359 ( 7804) covalent geometry : angle 0.50485 (10628) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.782 Fit side-chains REVERT: A 357 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7692 (mt0) REVERT: C 163 ARG cc_start: 0.7105 (mtp85) cc_final: 0.6896 (mtp85) REVERT: C 183 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7533 (mt-10) REVERT: D 292 ILE cc_start: 0.7453 (pp) cc_final: 0.7062 (pt) outliers start: 20 outliers final: 8 residues processed: 113 average time/residue: 1.2531 time to fit residues: 149.4893 Evaluate side-chains 107 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 325 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 64 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 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 = 0.3725 r_free = 0.3725 target = 0.115681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.082682 restraints weight = 12067.142| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.53 r_work: 0.3094 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1109 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 : 0.489 5.255 10628 Z= 0.255 Chirality : 0.040 0.122 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.213 10.521 1060 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.24 % Allowed : 19.04 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.28), residues: 988 helix: 2.41 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.29 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 232 HIS 0.002 0.001 HIS B 310 PHE 0.015 0.001 PHE D 336 TYR 0.008 0.001 TYR D 347 ARG 0.004 0.000 ARG B 294 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 559) hydrogen bonds : angle 3.51990 ( 1587) covalent geometry : bond 0.00331 ( 7804) covalent geometry : angle 0.48949 (10628) *********************** 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 131 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.833 Fit side-chains REVERT: A 154 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7834 (tp30) REVERT: A 357 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7748 (mt0) REVERT: C 163 ARG cc_start: 0.7216 (mtp85) cc_final: 0.6996 (mtp85) REVERT: C 183 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7838 (mt-10) outliers start: 25 outliers final: 7 residues processed: 122 average time/residue: 1.3516 time to fit residues: 173.4320 Evaluate side-chains 110 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 325 MET Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 325 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 12 optimal weight: 0.4980 chunk 42 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 55 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 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 = 0.3727 r_free = 0.3727 target = 0.115722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.082685 restraints weight = 11795.784| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.48 r_work: 0.3104 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1314 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= 0.120 Angle : 0.477 5.186 10628 Z= 0.248 Chirality : 0.039 0.120 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.174 11.143 1060 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.37 % Allowed : 19.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.28), residues: 988 helix: 2.50 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.29 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 232 HIS 0.001 0.000 HIS B 310 PHE 0.012 0.001 PHE B 336 TYR 0.010 0.001 TYR B 266 ARG 0.003 0.000 ARG B 294 Details of bonding type rmsd hydrogen bonds : bond 0.03180 ( 559) hydrogen bonds : angle 3.44695 ( 1587) covalent geometry : bond 0.00292 ( 7804) covalent geometry : angle 0.47698 (10628) *********************** 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 136 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.960 Fit side-chains REVERT: A 154 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7809 (tp30) REVERT: A 357 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7591 (mt0) REVERT: B 300 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7049 (mtp85) REVERT: B 322 LYS cc_start: 0.7511 (mttp) cc_final: 0.7286 (mptt) REVERT: C 163 ARG cc_start: 0.7188 (mtp85) cc_final: 0.6894 (mmm160) REVERT: C 183 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7738 (mt-10) REVERT: C 300 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7000 (mtp85) REVERT: D 292 ILE cc_start: 0.7665 (pp) cc_final: 0.7273 (pt) outliers start: 26 outliers final: 9 residues processed: 126 average time/residue: 1.3789 time to fit residues: 182.7262 Evaluate side-chains 116 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 325 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 54 optimal weight: 0.0030 chunk 50 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.115350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.082307 restraints weight = 11784.250| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.48 r_work: 0.3094 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1490 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= 0.128 Angle : 0.484 8.937 10628 Z= 0.248 Chirality : 0.040 0.120 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.150 10.955 1060 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.37 % Allowed : 19.43 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.28), residues: 988 helix: 2.49 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.37 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 232 HIS 0.001 0.000 HIS C 310 PHE 0.012 0.001 PHE B 336 TYR 0.010 0.001 TYR D 155 ARG 0.002 0.000 ARG B 294 Details of bonding type rmsd hydrogen bonds : bond 0.03158 ( 559) hydrogen bonds : angle 3.38759 ( 1587) covalent geometry : bond 0.00315 ( 7804) covalent geometry : angle 0.48367 (10628) *********************** 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 132 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.803 Fit side-chains REVERT: A 154 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7810 (tp30) REVERT: A 326 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7575 (ttt-90) REVERT: A 357 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7755 (mt0) REVERT: B 260 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7994 (mt) REVERT: B 300 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7149 (mtp85) REVERT: B 380 MET cc_start: 0.8273 (tmm) cc_final: 0.8019 (tmt) REVERT: C 163 ARG cc_start: 0.7188 (mtp85) cc_final: 0.6896 (mmm160) REVERT: C 183 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7673 (mt-10) REVERT: C 300 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.6927 (mtp85) REVERT: C 322 LYS cc_start: 0.7500 (mttp) cc_final: 0.7292 (mptt) outliers start: 26 outliers final: 13 residues processed: 122 average time/residue: 1.3257 time to fit residues: 170.2863 Evaluate side-chains 123 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain 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 260 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 325 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 56 optimal weight: 0.0670 chunk 72 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.115841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.083093 restraints weight = 11796.628| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.47 r_work: 0.3109 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1611 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= 0.108 Angle : 0.469 7.145 10628 Z= 0.241 Chirality : 0.039 0.120 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.094 10.984 1060 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.24 % Allowed : 20.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.28), residues: 988 helix: 2.59 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.44 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 232 HIS 0.001 0.000 HIS B 310 PHE 0.010 0.001 PHE B 336 TYR 0.011 0.001 TYR B 155 ARG 0.002 0.000 ARG B 294 Details of bonding type rmsd hydrogen bonds : bond 0.03005 ( 559) hydrogen bonds : angle 3.33855 ( 1587) covalent geometry : bond 0.00259 ( 7804) covalent geometry : angle 0.46917 (10628) *********************** 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: 25 poor density : 113 time to evaluate : 0.909 Fit side-chains REVERT: A 154 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7881 (tp30) REVERT: A 292 ILE cc_start: 0.6831 (pp) cc_final: 0.6282 (pt) REVERT: A 357 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7612 (mt0) REVERT: B 260 ILE cc_start: 0.8236 (mt) cc_final: 0.7995 (mt) REVERT: B 300 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7234 (mtp85) REVERT: B 380 MET cc_start: 0.8280 (tmm) cc_final: 0.8035 (tmt) REVERT: C 163 ARG cc_start: 0.7211 (mtp85) cc_final: 0.6948 (mmm160) REVERT: C 183 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7658 (mt-10) REVERT: C 300 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7160 (mtp85) REVERT: C 322 LYS cc_start: 0.7493 (mttp) cc_final: 0.7279 (mptt) REVERT: D 251 PHE cc_start: 0.8620 (m-10) cc_final: 0.8259 (m-80) REVERT: D 292 ILE cc_start: 0.7590 (pp) cc_final: 0.7238 (pt) REVERT: D 380 MET cc_start: 0.8188 (tmm) cc_final: 0.7974 (tmt) outliers start: 25 outliers final: 8 residues processed: 125 average time/residue: 1.3302 time to fit residues: 174.9159 Evaluate side-chains 120 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 298 LEU Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 325 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 53 optimal weight: 0.0980 chunk 32 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 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 = 0.3726 r_free = 0.3726 target = 0.115635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.082780 restraints weight = 11913.783| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.50 r_work: 0.3094 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1670 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= 0.123 Angle : 0.479 6.959 10628 Z= 0.247 Chirality : 0.039 0.119 1276 Planarity : 0.004 0.038 1308 Dihedral : 3.102 10.859 1060 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.76 % Allowed : 20.73 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.28), residues: 988 helix: 2.53 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.45 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 150 HIS 0.001 0.000 HIS C 310 PHE 0.012 0.001 PHE B 336 TYR 0.010 0.001 TYR D 155 ARG 0.002 0.000 ARG C 294 Details of bonding type rmsd hydrogen bonds : bond 0.03062 ( 559) hydrogen bonds : angle 3.32725 ( 1587) covalent geometry : bond 0.00302 ( 7804) covalent geometry : angle 0.47903 (10628) *********************** 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 140 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.802 Fit side-chains REVERT: A 154 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7826 (tp30) REVERT: A 292 ILE cc_start: 0.6847 (pp) cc_final: 0.6589 (pp) REVERT: A 294 ARG cc_start: 0.5662 (mtm180) cc_final: 0.5139 (mmt90) REVERT: A 326 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7518 (ttt-90) REVERT: A 357 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7576 (mt0) REVERT: B 154 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7800 (tp30) REVERT: B 260 ILE cc_start: 0.8225 (mt) cc_final: 0.7986 (mt) REVERT: B 300 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7211 (mtp85) REVERT: C 163 ARG cc_start: 0.7197 (mtp85) cc_final: 0.6924 (mmm160) REVERT: C 183 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7658 (mt-10) REVERT: C 300 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7169 (mtp85) REVERT: D 251 PHE cc_start: 0.8626 (m-10) cc_final: 0.8251 (m-80) REVERT: D 292 ILE cc_start: 0.7599 (pp) cc_final: 0.7254 (pt) REVERT: D 380 MET cc_start: 0.8207 (tmm) cc_final: 0.7960 (tmt) outliers start: 29 outliers final: 11 residues processed: 128 average time/residue: 1.4052 time to fit residues: 189.0190 Evaluate side-chains 125 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 419 ARG Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 325 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 6.9990 chunk 71 optimal weight: 0.0010 chunk 42 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 95 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 overall best weight: 0.4586 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.115886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.083099 restraints weight = 11923.815| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.50 r_work: 0.3110 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1728 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= 0.109 Angle : 0.488 6.778 10628 Z= 0.252 Chirality : 0.039 0.118 1276 Planarity : 0.004 0.038 1308 Dihedral : 3.077 10.986 1060 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.76 % Allowed : 20.98 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.11 (0.28), residues: 988 helix: 2.58 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.54 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 232 HIS 0.001 0.000 HIS B 310 PHE 0.010 0.001 PHE D 336 TYR 0.010 0.001 TYR B 155 ARG 0.005 0.000 ARG B 294 Details of bonding type rmsd hydrogen bonds : bond 0.02957 ( 559) hydrogen bonds : angle 3.30278 ( 1587) covalent geometry : bond 0.00263 ( 7804) covalent geometry : angle 0.48810 (10628) *********************** 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 : 0.876 Fit side-chains REVERT: A 154 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7800 (tp30) REVERT: A 292 ILE cc_start: 0.6889 (pp) cc_final: 0.6360 (pt) REVERT: A 294 ARG cc_start: 0.5611 (mtm180) cc_final: 0.5272 (mmt90) REVERT: A 326 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7491 (ttt-90) REVERT: A 357 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7513 (mt0) REVERT: B 154 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7732 (tp30) REVERT: B 300 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.7272 (mtp85) REVERT: B 380 MET cc_start: 0.8306 (tmm) cc_final: 0.8061 (tmt) REVERT: C 154 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7808 (tp30) REVERT: C 163 ARG cc_start: 0.7204 (mtp85) cc_final: 0.6945 (mmm160) REVERT: C 183 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7644 (mt-10) REVERT: C 300 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.7190 (mtp85) REVERT: D 251 PHE cc_start: 0.8631 (m-10) cc_final: 0.8225 (m-80) REVERT: D 292 ILE cc_start: 0.7598 (pp) cc_final: 0.7260 (pt) REVERT: D 303 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8169 (ptt-90) REVERT: D 380 MET cc_start: 0.8235 (tmm) cc_final: 0.7948 (tmt) outliers start: 29 outliers final: 11 residues processed: 125 average time/residue: 1.3514 time to fit residues: 177.6536 Evaluate side-chains 122 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 303 ARG Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 325 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 37 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 19 optimal weight: 0.1980 chunk 73 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.115157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.082445 restraints weight = 12067.796| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.49 r_work: 0.3101 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1797 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= 0.119 Angle : 0.489 6.601 10628 Z= 0.253 Chirality : 0.039 0.117 1276 Planarity : 0.004 0.038 1308 Dihedral : 3.077 10.769 1060 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.98 % Allowed : 21.89 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.28), residues: 988 helix: 2.54 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.60 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 232 HIS 0.001 0.000 HIS B 310 PHE 0.011 0.001 PHE B 336 TYR 0.011 0.001 TYR D 155 ARG 0.005 0.000 ARG B 294 Details of bonding type rmsd hydrogen bonds : bond 0.02991 ( 559) hydrogen bonds : angle 3.29530 ( 1587) covalent geometry : bond 0.00290 ( 7804) covalent geometry : angle 0.48923 (10628) *********************** 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 131 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.827 Fit side-chains REVERT: A 154 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7821 (tp30) REVERT: A 292 ILE cc_start: 0.6933 (pp) cc_final: 0.6400 (pt) REVERT: A 294 ARG cc_start: 0.5999 (mtm180) cc_final: 0.5619 (mmt90) REVERT: A 326 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7471 (ttt-90) REVERT: A 357 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7471 (mt0) REVERT: B 154 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7655 (tp30) REVERT: B 300 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7247 (mtp85) REVERT: C 154 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7824 (tp30) REVERT: C 163 ARG cc_start: 0.7218 (mtp85) cc_final: 0.6967 (mmm160) REVERT: C 183 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7649 (mt-10) REVERT: C 300 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7182 (mtp85) REVERT: C 326 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7444 (ttt-90) REVERT: D 251 PHE cc_start: 0.8624 (m-10) cc_final: 0.8250 (m-80) REVERT: D 260 ILE cc_start: 0.8271 (mt) cc_final: 0.7980 (mt) REVERT: D 292 ILE cc_start: 0.7602 (pp) cc_final: 0.7267 (pt) REVERT: D 303 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8173 (ptt-90) outliers start: 23 outliers final: 12 residues processed: 122 average time/residue: 1.3736 time to fit residues: 176.1155 Evaluate side-chains 126 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain B residue 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 292 ILE Chi-restraints excluded: chain C residue 298 LEU 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 303 ARG Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 325 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 89 optimal weight: 0.0980 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 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 = 0.3723 r_free = 0.3723 target = 0.115033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.082457 restraints weight = 12031.402| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.49 r_work: 0.3101 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7804 Z= 0.123 Angle : 0.502 6.600 10628 Z= 0.259 Chirality : 0.039 0.117 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.084 10.879 1060 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.24 % Allowed : 21.76 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.28), residues: 988 helix: 2.53 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.65 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 232 HIS 0.001 0.000 HIS B 310 PHE 0.010 0.001 PHE B 336 TYR 0.009 0.001 TYR B 155 ARG 0.005 0.000 ARG B 294 Details of bonding type rmsd hydrogen bonds : bond 0.02999 ( 559) hydrogen bonds : angle 3.30852 ( 1587) covalent geometry : bond 0.00304 ( 7804) covalent geometry : angle 0.50215 (10628) ********************** 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 133 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.950 Fit side-chains REVERT: A 154 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7830 (tp30) REVERT: A 292 ILE cc_start: 0.6947 (pp) cc_final: 0.6420 (pt) REVERT: A 294 ARG cc_start: 0.6137 (mtm180) cc_final: 0.5687 (tpp80) REVERT: A 326 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7457 (ttt-90) REVERT: A 357 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7456 (mt0) REVERT: B 154 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7642 (tp30) REVERT: B 300 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7237 (mtp85) REVERT: C 154 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7754 (tp30) REVERT: C 163 ARG cc_start: 0.7222 (mtp85) cc_final: 0.6976 (mmm160) REVERT: C 183 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7651 (mt-10) REVERT: C 300 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7176 (mtp85) REVERT: C 326 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7464 (ttt-90) REVERT: C 380 MET cc_start: 0.8231 (tmm) cc_final: 0.8030 (tmt) REVERT: D 251 PHE cc_start: 0.8622 (m-10) cc_final: 0.8227 (m-80) REVERT: D 260 ILE cc_start: 0.8220 (mt) cc_final: 0.7928 (mt) REVERT: D 292 ILE cc_start: 0.7557 (pp) cc_final: 0.7220 (pt) REVERT: D 303 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8173 (ptt-90) outliers start: 25 outliers final: 12 residues processed: 122 average time/residue: 1.5365 time to fit residues: 197.2680 Evaluate side-chains 124 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 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 298 LEU 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 303 ARG Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 325 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 80 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 96 optimal weight: 0.4980 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.114866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.082463 restraints weight = 11959.943| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.47 r_work: 0.3092 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1854 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= 0.128 Angle : 0.498 6.442 10628 Z= 0.257 Chirality : 0.039 0.119 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.104 10.755 1060 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.24 % Allowed : 21.76 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.11 (0.28), residues: 988 helix: 2.53 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.70 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 232 HIS 0.001 0.000 HIS C 310 PHE 0.011 0.001 PHE C 336 TYR 0.012 0.001 TYR D 155 ARG 0.005 0.000 ARG B 294 Details of bonding type rmsd hydrogen bonds : bond 0.03035 ( 559) hydrogen bonds : angle 3.29123 ( 1587) covalent geometry : bond 0.00319 ( 7804) covalent geometry : angle 0.49829 (10628) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6894.84 seconds wall clock time: 119 minutes 42.16 seconds (7182.16 seconds total)