Starting phenix.real_space_refine on Tue Sep 24 08:58:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vch_43136/09_2024/8vch_43136.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vch_43136/09_2024/8vch_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vch_43136/09_2024/8vch_43136.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vch_43136/09_2024/8vch_43136.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vch_43136/09_2024/8vch_43136.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vch_43136/09_2024/8vch_43136.cif" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 32 5.16 5 C 5104 2.51 5 N 1192 2.21 5 O 1284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.03, per 1000 atoms: 0.66 Number of scatterers: 7614 At special positions: 0 Unit cell: (101.46, 101.46, 71.556, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 2 19.00 S 32 16.00 O 1284 8.00 N 1192 7.00 C 5104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 1.0 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: 0.70 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: 1.92 Time building geometry restraints manager: 2.18 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: 0.00 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.050 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7804 Z= 0.229 Angle : 0.578 5.820 10628 Z= 0.335 Chirality : 0.041 0.117 1276 Planarity : 0.004 0.045 1308 Dihedral : 15.042 82.339 2596 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.78 % Allowed : 17.23 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.27), residues: 988 helix: 2.03 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -0.36 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 150 HIS 0.002 0.001 HIS A 310 PHE 0.016 0.001 PHE B 153 TYR 0.012 0.002 TYR A 155 ARG 0.005 0.001 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 0.771 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: 1.2761 time to fit residues: 148.0415 Evaluate side-chains 100 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7804 Z= 0.229 Angle : 0.505 5.299 10628 Z= 0.266 Chirality : 0.040 0.129 1276 Planarity : 0.005 0.040 1308 Dihedral : 3.571 34.984 1065 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.59 % Allowed : 16.97 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.29), residues: 988 helix: 2.27 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.36 (0.44), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 232 HIS 0.002 0.001 HIS B 310 PHE 0.016 0.001 PHE D 336 TYR 0.009 0.001 TYR D 347 ARG 0.004 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.903 Fit side-chains REVERT: A 357 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7676 (mt0) REVERT: C 163 ARG cc_start: 0.7099 (mtp85) cc_final: 0.6886 (mtp85) REVERT: C 183 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7514 (mt-10) REVERT: D 292 ILE cc_start: 0.7457 (pp) cc_final: 0.7068 (pt) outliers start: 20 outliers final: 8 residues processed: 113 average time/residue: 1.1852 time to fit residues: 141.7898 Evaluate side-chains 107 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 50 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1122 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= 0.205 Angle : 0.485 5.245 10628 Z= 0.252 Chirality : 0.040 0.121 1276 Planarity : 0.004 0.040 1308 Dihedral : 3.210 10.557 1060 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.56 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: 2.85 (0.28), residues: 988 helix: 2.42 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.31 (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 B 266 ARG 0.003 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 0.804 Fit side-chains REVERT: A 154 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7729 (tp30) REVERT: A 357 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7666 (mt0) REVERT: C 163 ARG cc_start: 0.7095 (mtp85) cc_final: 0.6879 (mtp85) REVERT: C 183 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7590 (mt-10) REVERT: D 292 ILE cc_start: 0.7618 (pp) cc_final: 0.7223 (pt) outliers start: 25 outliers final: 7 residues processed: 123 average time/residue: 1.2723 time to fit residues: 164.9252 Evaluate side-chains 111 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 68 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1342 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= 0.210 Angle : 0.487 5.241 10628 Z= 0.253 Chirality : 0.040 0.121 1276 Planarity : 0.004 0.040 1308 Dihedral : 3.203 11.202 1060 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.37 % Allowed : 19.82 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.28), residues: 988 helix: 2.46 (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 0.001 0.000 HIS C 310 PHE 0.013 0.001 PHE B 336 TYR 0.007 0.001 TYR D 347 ARG 0.003 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 0.821 Fit side-chains REVERT: A 154 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7654 (tp30) REVERT: A 357 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7481 (mt0) REVERT: B 300 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7043 (mtp85) REVERT: C 163 ARG cc_start: 0.7079 (mtp85) cc_final: 0.6870 (mtp85) REVERT: C 183 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7471 (mt-10) REVERT: C 300 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7030 (mtp85) REVERT: D 260 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7933 (mt) outliers start: 26 outliers final: 8 residues processed: 123 average time/residue: 1.2797 time to fit residues: 165.9262 Evaluate side-chains 114 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 66 optimal weight: 0.2980 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1484 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= 0.185 Angle : 0.475 8.690 10628 Z= 0.243 Chirality : 0.039 0.119 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.128 11.068 1060 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.11 % Allowed : 19.69 % 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: 2.99 (0.28), residues: 988 helix: 2.52 (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 0.011 0.001 PHE B 336 TYR 0.010 0.001 TYR D 155 ARG 0.003 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 0.852 Fit side-chains REVERT: A 154 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7658 (tp30) REVERT: A 292 ILE cc_start: 0.7217 (pp) cc_final: 0.6666 (pt) REVERT: A 326 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7343 (ttt-90) REVERT: A 357 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7646 (mt0) REVERT: B 260 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7864 (mt) REVERT: B 300 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7097 (mtp85) REVERT: B 380 MET cc_start: 0.8148 (tmm) cc_final: 0.7888 (tmt) REVERT: C 163 ARG cc_start: 0.7064 (mtp85) cc_final: 0.6788 (mmm160) REVERT: C 183 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7403 (mt-10) REVERT: C 300 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.6907 (mtp85) REVERT: D 260 ILE cc_start: 0.8247 (mt) cc_final: 0.7950 (mt) outliers start: 24 outliers final: 10 residues processed: 122 average time/residue: 1.2805 time to fit residues: 164.5861 Evaluate side-chains 122 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain C residue 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 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 19 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1621 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= 0.205 Angle : 0.486 6.855 10628 Z= 0.250 Chirality : 0.040 0.119 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.136 11.127 1060 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.37 % Allowed : 20.47 % 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 (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: 2.96 (0.28), residues: 988 helix: 2.49 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.41 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 232 HIS 0.001 0.000 HIS C 310 PHE 0.012 0.001 PHE D 336 TYR 0.010 0.001 TYR B 155 ARG 0.002 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 0.851 Fit side-chains REVERT: A 154 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7726 (tp30) REVERT: A 292 ILE cc_start: 0.6760 (pp) cc_final: 0.6510 (pp) REVERT: A 294 ARG cc_start: 0.5662 (mtm180) cc_final: 0.5119 (mmt90) REVERT: A 326 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7302 (ttt-90) REVERT: A 357 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7541 (mt0) REVERT: B 260 ILE cc_start: 0.8079 (mt) cc_final: 0.7829 (mt) REVERT: B 300 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7009 (mtp85) REVERT: C 154 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7598 (tp30) REVERT: C 163 ARG cc_start: 0.7084 (mtp85) cc_final: 0.6810 (mmm160) REVERT: C 183 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7400 (mt-10) REVERT: C 300 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.6881 (mtp85) REVERT: D 251 PHE cc_start: 0.8561 (m-10) cc_final: 0.8178 (m-80) REVERT: D 260 ILE cc_start: 0.8233 (mt) cc_final: 0.7950 (mt) REVERT: D 292 ILE cc_start: 0.7524 (pp) cc_final: 0.7172 (pt) REVERT: D 380 MET cc_start: 0.8136 (tmm) cc_final: 0.7928 (tmt) outliers start: 26 outliers final: 12 residues processed: 130 average time/residue: 1.3041 time to fit residues: 178.2788 Evaluate side-chains 126 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 372 MET 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 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 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 55 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1704 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= 0.247 Angle : 0.505 6.818 10628 Z= 0.260 Chirality : 0.040 0.129 1276 Planarity : 0.004 0.040 1308 Dihedral : 3.181 10.999 1060 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.15 % Allowed : 20.21 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.28), residues: 988 helix: 2.42 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.43 (0.44), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 232 HIS 0.001 0.001 HIS B 310 PHE 0.013 0.001 PHE B 336 TYR 0.010 0.001 TYR C 155 ARG 0.005 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 109 time to evaluate : 0.866 Fit side-chains REVERT: A 154 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7660 (tp30) REVERT: A 292 ILE cc_start: 0.6854 (pp) cc_final: 0.6614 (pp) REVERT: A 326 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7341 (ttt-90) REVERT: A 357 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7501 (mt0) REVERT: A 372 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8860 (mtm) REVERT: B 260 ILE cc_start: 0.8053 (mt) cc_final: 0.7819 (mt) REVERT: B 300 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.6882 (mtp85) REVERT: C 154 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7596 (tp30) REVERT: C 183 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7424 (mt-10) REVERT: C 300 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.6872 (mtp85) REVERT: D 251 PHE cc_start: 0.8551 (m-10) cc_final: 0.8173 (m-80) REVERT: D 260 ILE cc_start: 0.8194 (mt) cc_final: 0.7914 (mt) REVERT: D 292 ILE cc_start: 0.7517 (pp) cc_final: 0.7167 (pt) REVERT: D 303 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7996 (ptt-90) REVERT: D 380 MET cc_start: 0.8217 (tmm) cc_final: 0.8010 (tmt) outliers start: 32 outliers final: 15 residues processed: 130 average time/residue: 1.2974 time to fit residues: 177.7076 Evaluate side-chains 129 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 372 MET 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 C residue 292 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 303 ARG Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 325 MET 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 29 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 84 optimal weight: 0.0270 chunk 89 optimal weight: 2.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1766 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= 0.173 Angle : 0.484 6.687 10628 Z= 0.249 Chirality : 0.039 0.119 1276 Planarity : 0.004 0.040 1308 Dihedral : 3.117 11.112 1060 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.28), residues: 988 helix: 2.56 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.46 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 232 HIS 0.001 0.000 HIS C 310 PHE 0.010 0.001 PHE D 336 TYR 0.006 0.001 TYR D 347 ARG 0.005 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 0.859 Fit side-chains REVERT: A 154 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7625 (tp30) REVERT: A 292 ILE cc_start: 0.6886 (pp) cc_final: 0.6366 (pt) REVERT: A 294 ARG cc_start: 0.5942 (mtm-85) cc_final: 0.5437 (mmt90) REVERT: A 357 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7414 (mt0) REVERT: B 154 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7634 (tp30) REVERT: B 300 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7104 (mtp85) REVERT: C 154 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7668 (tp30) REVERT: C 183 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7391 (mt-10) REVERT: C 300 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7020 (mtp85) REVERT: D 251 PHE cc_start: 0.8560 (m-10) cc_final: 0.8167 (m-80) REVERT: D 292 ILE cc_start: 0.7536 (pp) cc_final: 0.7195 (pt) REVERT: D 380 MET cc_start: 0.8195 (tmm) cc_final: 0.7892 (tmt) outliers start: 22 outliers final: 9 residues processed: 119 average time/residue: 1.2826 time to fit residues: 160.8984 Evaluate side-chains 117 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 372 MET 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 261 VAL 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 92 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1811 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= 0.225 Angle : 0.494 6.419 10628 Z= 0.255 Chirality : 0.040 0.119 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.160 10.991 1060 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.24 % Allowed : 21.63 % 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: 2.94 (0.28), residues: 988 helix: 2.46 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.46 (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 0.013 0.001 PHE C 336 TYR 0.010 0.001 TYR D 155 ARG 0.005 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 0.854 Fit side-chains REVERT: A 154 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7785 (tp30) REVERT: A 292 ILE cc_start: 0.6906 (pp) cc_final: 0.6670 (pp) REVERT: A 294 ARG cc_start: 0.6025 (mtm-85) cc_final: 0.5693 (mmt90) REVERT: A 326 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7317 (ttt-90) REVERT: A 357 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7374 (mt0) REVERT: A 372 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8861 (mtm) REVERT: B 154 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7721 (tp30) REVERT: B 300 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7075 (mtp85) REVERT: C 154 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7564 (tp30) REVERT: C 183 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7413 (mt-10) REVERT: C 300 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.6882 (mtp85) REVERT: C 326 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7309 (ttt-90) REVERT: D 251 PHE cc_start: 0.8565 (m-10) cc_final: 0.8157 (m-80) REVERT: D 292 ILE cc_start: 0.7530 (pp) cc_final: 0.7191 (pt) REVERT: D 380 MET cc_start: 0.8261 (tmm) cc_final: 0.8010 (tmt) outliers start: 25 outliers final: 13 residues processed: 120 average time/residue: 1.3188 time to fit residues: 166.5947 Evaluate side-chains 125 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 372 MET Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 326 ARG Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 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 45 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1824 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= 0.193 Angle : 0.483 6.438 10628 Z= 0.249 Chirality : 0.039 0.118 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.140 11.071 1060 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.24 % Allowed : 21.50 % 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: 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 TRP 0.006 0.001 TRP A 232 HIS 0.001 0.000 HIS C 310 PHE 0.011 0.001 PHE C 336 TYR 0.006 0.001 TYR A 266 ARG 0.005 0.000 ARG B 294 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 0.961 Fit side-chains REVERT: A 154 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7768 (tp30) REVERT: A 273 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6426 (pt0) REVERT: A 292 ILE cc_start: 0.6922 (pp) cc_final: 0.6412 (pt) REVERT: A 294 ARG cc_start: 0.6171 (mtm-85) cc_final: 0.5861 (mmt90) REVERT: A 326 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7283 (ttt-90) REVERT: A 357 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7336 (mt0) REVERT: A 372 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8856 (mtm) REVERT: B 154 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7639 (tp30) REVERT: B 300 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7089 (mtp85) REVERT: C 154 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7662 (tp30) REVERT: C 183 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7393 (mt-10) REVERT: C 300 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.6994 (mtp85) REVERT: C 326 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7301 (ttt-90) REVERT: D 251 PHE cc_start: 0.8587 (m-10) cc_final: 0.8161 (m-80) REVERT: D 292 ILE cc_start: 0.7526 (pp) cc_final: 0.7166 (pt) REVERT: D 380 MET cc_start: 0.8273 (tmm) cc_final: 0.8016 (tmt) outliers start: 25 outliers final: 11 residues processed: 120 average time/residue: 1.2845 time to fit residues: 162.5032 Evaluate side-chains 122 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 372 MET Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 300 ARG Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 326 ARG Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain D residue 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 73 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 57 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.114197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.081802 restraints weight = 11744.296| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.42 r_work: 0.3092 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1891 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= 0.206 Angle : 0.491 6.357 10628 Z= 0.253 Chirality : 0.040 0.119 1276 Planarity : 0.004 0.039 1308 Dihedral : 3.134 10.943 1060 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.59 % Allowed : 22.28 % 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: 2.99 (0.28), residues: 988 helix: 2.48 (0.20), residues: 736 sheet: None (None), residues: 0 loop : 0.53 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 232 HIS 0.001 0.000 HIS C 310 PHE 0.011 0.001 PHE D 336 TYR 0.010 0.001 TYR C 155 ARG 0.005 0.000 ARG B 294 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3161.90 seconds wall clock time: 55 minutes 52.93 seconds (3352.93 seconds total)