Starting phenix.real_space_refine on Tue Feb 13 08:53:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lto_23517/02_2024/7lto_23517.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lto_23517/02_2024/7lto_23517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lto_23517/02_2024/7lto_23517.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lto_23517/02_2024/7lto_23517.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lto_23517/02_2024/7lto_23517.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lto_23517/02_2024/7lto_23517.pdb" } resolution = 3.2 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= 0.003 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: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 3114 2.51 5 N 776 2.21 5 O 838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "A ARG 97": "NH1" <-> "NH2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ASP 379": "OD1" <-> "OD2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 500": "OE1" <-> "OE2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B ARG 318": "NH1" <-> "NH2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4754 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2876 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 15, 'TRANS': 351} Chain breaks: 4 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 97 Chain: "B" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1878 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 232} Chain breaks: 5 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 119 Time building chain proxies: 3.20, per 1000 atoms: 0.67 Number of scatterers: 4754 At special positions: 0 Unit cell: (64.904, 77.672, 101.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 838 8.00 N 776 7.00 C 3114 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 - 3.50 Amino acid : False - 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: 1.86 Conformation dependent library (CDL) restraints added in 853.4 milliseconds 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1184 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 58.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 25 through 41 removed outlier: 3.660A pdb=" N LEU A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 53 removed outlier: 3.793A pdb=" N LEU A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 76 removed outlier: 3.971A pdb=" N VAL A 71 " --> pdb=" O ASP A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 91 removed outlier: 4.030A pdb=" N LEU A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 Processing helix chain 'A' and resid 126 through 140 removed outlier: 3.775A pdb=" N ALA A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 229 through 239 Processing helix chain 'A' and resid 239 through 255 removed outlier: 3.920A pdb=" N CYS A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 260 removed outlier: 3.985A pdb=" N GLN A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.714A pdb=" N PHE A 297 " --> pdb=" O PHE A 293 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 363 removed outlier: 4.329A pdb=" N LEU A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 362 " --> pdb=" O CYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 391 Processing helix chain 'A' and resid 394 through 403 removed outlier: 3.936A pdb=" N PHE A 402 " --> pdb=" O PHE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 430 removed outlier: 3.550A pdb=" N GLU A 424 " --> pdb=" O GLY A 420 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LYS A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 511 removed outlier: 3.569A pdb=" N ASP A 504 " --> pdb=" O GLU A 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 217 Processing helix chain 'B' and resid 219 through 225 Processing helix chain 'B' and resid 245 through 253 Processing helix chain 'B' and resid 283 through 292 removed outlier: 3.513A pdb=" N MET B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 317 removed outlier: 3.541A pdb=" N ARG B 304 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP B 317 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 322 Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'B' and resid 339 through 346 Processing helix chain 'B' and resid 354 through 366 removed outlier: 4.065A pdb=" N LEU B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 361 " --> pdb=" O PHE B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 removed outlier: 3.663A pdb=" N ARG B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ARG B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 397 Processing helix chain 'B' and resid 404 through 416 Processing helix chain 'B' and resid 432 through 441 removed outlier: 3.753A pdb=" N CYS B 436 " --> pdb=" O TYR B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 462 removed outlier: 4.018A pdb=" N LEU B 453 " --> pdb=" O GLU B 449 " (cutoff:3.500A) 203 hydrogen bonds defined for protein. 609 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: 1.10 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1470 1.34 - 1.46: 861 1.46 - 1.58: 2484 1.58 - 1.70: 0 1.70 - 1.82: 38 Bond restraints: 4853 Sorted by residual: bond pdb=" CA GLU A 193 " pdb=" C GLU A 193 " ideal model delta sigma weight residual 1.524 1.556 -0.032 1.24e-02 6.50e+03 6.64e+00 bond pdb=" CA LEU A 192 " pdb=" C LEU A 192 " ideal model delta sigma weight residual 1.522 1.545 -0.023 1.25e-02 6.40e+03 3.33e+00 bond pdb=" CA ALA B 323 " pdb=" C ALA B 323 " ideal model delta sigma weight residual 1.530 1.511 0.020 1.23e-02 6.61e+03 2.58e+00 bond pdb=" C MET A 241 " pdb=" O MET A 241 " ideal model delta sigma weight residual 1.244 1.228 0.016 1.00e-02 1.00e+04 2.43e+00 bond pdb=" C TRP A 240 " pdb=" O TRP A 240 " ideal model delta sigma weight residual 1.236 1.219 0.018 1.29e-02 6.01e+03 1.85e+00 ... (remaining 4848 not shown) Histogram of bond angle deviations from ideal: 100.08 - 106.90: 112 106.90 - 113.71: 2677 113.71 - 120.53: 1949 120.53 - 127.34: 1787 127.34 - 134.16: 38 Bond angle restraints: 6563 Sorted by residual: angle pdb=" N GLN A 194 " pdb=" CA GLN A 194 " pdb=" C GLN A 194 " ideal model delta sigma weight residual 112.57 119.12 -6.55 1.13e+00 7.83e-01 3.36e+01 angle pdb=" N TRP A 240 " pdb=" CA TRP A 240 " pdb=" C TRP A 240 " ideal model delta sigma weight residual 112.23 119.19 -6.96 1.26e+00 6.30e-01 3.06e+01 angle pdb=" C ASP A 91 " pdb=" N PRO A 92 " pdb=" CA PRO A 92 " ideal model delta sigma weight residual 119.24 124.34 -5.10 1.04e+00 9.25e-01 2.40e+01 angle pdb=" N LEU A 192 " pdb=" CA LEU A 192 " pdb=" C LEU A 192 " ideal model delta sigma weight residual 114.09 106.86 7.23 1.55e+00 4.16e-01 2.17e+01 angle pdb=" N LEU A 131 " pdb=" CA LEU A 131 " pdb=" C LEU A 131 " ideal model delta sigma weight residual 112.04 105.82 6.22 1.44e+00 4.82e-01 1.86e+01 ... (remaining 6558 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 2596 17.82 - 35.64: 241 35.64 - 53.46: 58 53.46 - 71.28: 10 71.28 - 89.11: 5 Dihedral angle restraints: 2910 sinusoidal: 1106 harmonic: 1804 Sorted by residual: dihedral pdb=" CA GLU B 398 " pdb=" C GLU B 398 " pdb=" N PHE B 399 " pdb=" CA PHE B 399 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA SER A 411 " pdb=" C SER A 411 " pdb=" N TYR A 412 " pdb=" CA TYR A 412 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ASN B 345 " pdb=" C ASN B 345 " pdb=" N SER B 346 " pdb=" CA SER B 346 " ideal model delta harmonic sigma weight residual 180.00 163.22 16.78 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 2907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 695 0.075 - 0.150: 54 0.150 - 0.225: 7 0.225 - 0.299: 3 0.299 - 0.374: 1 Chirality restraints: 760 Sorted by residual: chirality pdb=" CA TRP A 240 " pdb=" N TRP A 240 " pdb=" C TRP A 240 " pdb=" CB TRP A 240 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CA TYR A 81 " pdb=" N TYR A 81 " pdb=" C TYR A 81 " pdb=" CB TYR A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA TYR A 82 " pdb=" N TYR A 82 " pdb=" C TYR A 82 " pdb=" CB TYR A 82 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 757 not shown) Planarity restraints: 819 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 193 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C GLU A 193 " -0.031 2.00e-02 2.50e+03 pdb=" O GLU A 193 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN A 194 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 411 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C SER A 411 " 0.029 2.00e-02 2.50e+03 pdb=" O SER A 411 " -0.011 2.00e-02 2.50e+03 pdb=" N TYR A 412 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 239 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C ILE A 239 " 0.028 2.00e-02 2.50e+03 pdb=" O ILE A 239 " -0.011 2.00e-02 2.50e+03 pdb=" N TRP A 240 " -0.009 2.00e-02 2.50e+03 ... (remaining 816 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 929 2.77 - 3.30: 4572 3.30 - 3.83: 7256 3.83 - 4.37: 9095 4.37 - 4.90: 15381 Nonbonded interactions: 37233 Sorted by model distance: nonbonded pdb=" O PHE A 50 " pdb=" NE2 GLN A 54 " model vdw 2.232 2.520 nonbonded pdb=" O ARG A 387 " pdb=" OG SER A 391 " model vdw 2.281 2.440 nonbonded pdb=" O LYS A 343 " pdb=" OG SER A 347 " model vdw 2.282 2.440 nonbonded pdb=" NZ LYS A 207 " pdb=" O VAL A 321 " model vdw 2.311 2.520 nonbonded pdb=" NE2 GLN B 370 " pdb=" O THR B 414 " model vdw 2.311 2.520 ... (remaining 37228 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.640 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: 4.990 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 17.210 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 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 : 0.003 0.032 4853 Z= 0.219 Angle : 0.707 7.229 6563 Z= 0.447 Chirality : 0.049 0.374 760 Planarity : 0.003 0.037 819 Dihedral : 15.408 89.105 1726 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 3.25 % Allowed : 15.45 % Favored : 81.30 % 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: -4.26 (0.29), residues: 583 helix: -2.13 (0.25), residues: 333 sheet: None (None), residues: 0 loop : -3.81 (0.31), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 200 HIS 0.002 0.000 HIS A 46 PHE 0.011 0.001 PHE A 413 TYR 0.009 0.001 TYR A 82 ARG 0.001 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 337 LYS cc_start: 0.8674 (mttm) cc_final: 0.8441 (mmmt) outliers start: 16 outliers final: 11 residues processed: 111 average time/residue: 0.1847 time to fit residues: 25.5353 Evaluate side-chains 88 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.0970 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 90 ASN A 94 ASN A 134 GLN A 345 GLN A 383 GLN B 201 HIS B 206 ASN B 211 GLN B 277 ASN B 389 GLN B 407 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4853 Z= 0.193 Angle : 0.562 6.730 6563 Z= 0.287 Chirality : 0.040 0.144 760 Planarity : 0.004 0.040 819 Dihedral : 6.440 51.571 660 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 3.05 % Allowed : 19.11 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.75 (0.32), residues: 583 helix: -0.75 (0.28), residues: 344 sheet: None (None), residues: 0 loop : -3.51 (0.32), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 240 HIS 0.003 0.001 HIS A 46 PHE 0.012 0.001 PHE B 343 TYR 0.021 0.001 TYR B 432 ARG 0.002 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.577 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 96 average time/residue: 0.1417 time to fit residues: 18.0187 Evaluate side-chains 91 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 0.0980 chunk 16 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 53 optimal weight: 0.2980 chunk 57 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4853 Z= 0.153 Angle : 0.522 7.197 6563 Z= 0.262 Chirality : 0.039 0.127 760 Planarity : 0.003 0.042 819 Dihedral : 5.640 49.462 650 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 3.25 % Allowed : 20.53 % Favored : 76.22 % 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: -1.80 (0.34), residues: 583 helix: 0.02 (0.29), residues: 348 sheet: None (None), residues: 0 loop : -3.17 (0.33), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 240 HIS 0.001 0.000 HIS B 359 PHE 0.014 0.001 PHE B 396 TYR 0.008 0.001 TYR A 82 ARG 0.002 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 387 ARG cc_start: 0.7866 (ttm110) cc_final: 0.7616 (ttp-110) REVERT: B 369 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8422 (pp) outliers start: 16 outliers final: 9 residues processed: 100 average time/residue: 0.1415 time to fit residues: 18.7378 Evaluate side-chains 96 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 395 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 57 optimal weight: 0.1980 chunk 28 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4853 Z= 0.178 Angle : 0.536 6.824 6563 Z= 0.267 Chirality : 0.039 0.122 760 Planarity : 0.003 0.045 819 Dihedral : 5.116 47.927 647 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 4.27 % Allowed : 20.33 % Favored : 75.41 % 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: -1.40 (0.34), residues: 583 helix: 0.34 (0.29), residues: 343 sheet: None (None), residues: 0 loop : -2.92 (0.34), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 240 HIS 0.001 0.000 HIS B 359 PHE 0.012 0.001 PHE B 343 TYR 0.019 0.001 TYR B 432 ARG 0.001 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: B 369 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8391 (pp) REVERT: B 450 ILE cc_start: 0.6923 (mp) cc_final: 0.6397 (mp) outliers start: 21 outliers final: 16 residues processed: 103 average time/residue: 0.1437 time to fit residues: 19.6901 Evaluate side-chains 102 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 29 optimal weight: 0.0270 chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4853 Z= 0.160 Angle : 0.541 11.998 6563 Z= 0.266 Chirality : 0.039 0.122 760 Planarity : 0.003 0.045 819 Dihedral : 5.040 48.087 647 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.86 % Allowed : 20.53 % Favored : 75.61 % 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: -1.13 (0.35), residues: 583 helix: 0.55 (0.30), residues: 343 sheet: None (None), residues: 0 loop : -2.80 (0.34), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 200 HIS 0.001 0.000 HIS B 342 PHE 0.011 0.001 PHE B 343 TYR 0.012 0.001 TYR B 209 ARG 0.002 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 369 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8429 (pp) REVERT: B 450 ILE cc_start: 0.6942 (mp) cc_final: 0.6409 (mp) outliers start: 19 outliers final: 14 residues processed: 102 average time/residue: 0.1378 time to fit residues: 18.6136 Evaluate side-chains 100 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 0.9990 chunk 57 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN A 508 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4853 Z= 0.187 Angle : 0.595 16.340 6563 Z= 0.284 Chirality : 0.039 0.121 760 Planarity : 0.003 0.045 819 Dihedral : 5.057 50.269 647 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 3.86 % Allowed : 20.93 % Favored : 75.20 % 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: -1.01 (0.35), residues: 583 helix: 0.61 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -2.72 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 240 HIS 0.001 0.000 HIS B 342 PHE 0.014 0.001 PHE B 307 TYR 0.020 0.001 TYR B 432 ARG 0.002 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: B 369 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8392 (pp) REVERT: B 450 ILE cc_start: 0.6942 (mp) cc_final: 0.6420 (mp) outliers start: 19 outliers final: 18 residues processed: 101 average time/residue: 0.1408 time to fit residues: 18.8726 Evaluate side-chains 105 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.0170 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4853 Z= 0.173 Angle : 0.587 15.218 6563 Z= 0.280 Chirality : 0.039 0.120 760 Planarity : 0.003 0.045 819 Dihedral : 4.775 52.703 645 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 4.27 % Allowed : 21.95 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.35), residues: 583 helix: 0.69 (0.30), residues: 346 sheet: None (None), residues: 0 loop : -2.62 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 200 HIS 0.001 0.000 HIS B 359 PHE 0.013 0.001 PHE B 343 TYR 0.014 0.001 TYR A 412 ARG 0.001 0.000 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: B 336 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6871 (mt-10) REVERT: B 369 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8408 (pp) REVERT: B 450 ILE cc_start: 0.6929 (mp) cc_final: 0.6414 (mp) outliers start: 21 outliers final: 17 residues processed: 99 average time/residue: 0.1355 time to fit residues: 17.9437 Evaluate side-chains 103 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 0.0670 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 49 optimal weight: 0.0670 chunk 52 optimal weight: 0.0470 chunk 31 optimal weight: 0.8980 overall best weight: 0.3554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 277 ASN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4853 Z= 0.150 Angle : 0.581 14.419 6563 Z= 0.276 Chirality : 0.038 0.116 760 Planarity : 0.003 0.045 819 Dihedral : 4.644 53.395 645 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.47 % Allowed : 22.15 % Favored : 73.37 % 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: -0.71 (0.35), residues: 583 helix: 0.84 (0.30), residues: 347 sheet: None (None), residues: 0 loop : -2.59 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 200 HIS 0.001 0.000 HIS B 359 PHE 0.010 0.001 PHE B 343 TYR 0.018 0.001 TYR B 432 ARG 0.002 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: A 53 CYS cc_start: 0.8164 (p) cc_final: 0.7730 (p) REVERT: B 292 MET cc_start: 0.7030 (ttp) cc_final: 0.6816 (ttt) REVERT: B 369 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8386 (pp) REVERT: B 450 ILE cc_start: 0.6901 (OUTLIER) cc_final: 0.6365 (mp) outliers start: 22 outliers final: 19 residues processed: 99 average time/residue: 0.1431 time to fit residues: 18.8834 Evaluate side-chains 107 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 450 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 3.9990 chunk 41 optimal weight: 0.0870 chunk 16 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 0.0070 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 58 optimal weight: 0.0270 overall best weight: 0.3434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 277 ASN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4853 Z= 0.144 Angle : 0.567 13.802 6563 Z= 0.271 Chirality : 0.039 0.132 760 Planarity : 0.003 0.045 819 Dihedral : 4.578 53.836 645 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 4.47 % Allowed : 21.95 % Favored : 73.58 % 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: -0.55 (0.36), residues: 583 helix: 0.94 (0.30), residues: 348 sheet: None (None), residues: 0 loop : -2.49 (0.37), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 200 HIS 0.001 0.000 HIS B 359 PHE 0.011 0.001 PHE A 55 TYR 0.013 0.001 TYR A 412 ARG 0.001 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 53 CYS cc_start: 0.8155 (p) cc_final: 0.7719 (p) REVERT: B 292 MET cc_start: 0.7050 (ttp) cc_final: 0.6848 (ttt) REVERT: B 336 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6830 (mt-10) REVERT: B 369 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8368 (pp) REVERT: B 450 ILE cc_start: 0.6898 (OUTLIER) cc_final: 0.6380 (mp) outliers start: 22 outliers final: 19 residues processed: 100 average time/residue: 0.1419 time to fit residues: 18.9091 Evaluate side-chains 107 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 450 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 0.0370 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 277 ASN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4853 Z= 0.188 Angle : 0.605 13.863 6563 Z= 0.294 Chirality : 0.040 0.232 760 Planarity : 0.003 0.043 819 Dihedral : 4.743 56.217 645 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.47 % Allowed : 22.97 % Favored : 72.56 % 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: -0.61 (0.35), residues: 583 helix: 0.88 (0.29), residues: 346 sheet: None (None), residues: 0 loop : -2.46 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 240 HIS 0.001 0.000 HIS B 368 PHE 0.013 0.001 PHE B 343 TYR 0.020 0.001 TYR B 432 ARG 0.002 0.000 ARG A 387 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 86 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 53 CYS cc_start: 0.8194 (p) cc_final: 0.7703 (p) REVERT: B 217 MET cc_start: 0.5884 (mmm) cc_final: 0.5663 (mmm) REVERT: B 292 MET cc_start: 0.7057 (ttp) cc_final: 0.6845 (ttt) REVERT: B 336 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6830 (mt-10) REVERT: B 369 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8424 (pp) REVERT: B 450 ILE cc_start: 0.6937 (OUTLIER) cc_final: 0.6410 (mp) outliers start: 22 outliers final: 19 residues processed: 97 average time/residue: 0.1420 time to fit residues: 18.3519 Evaluate side-chains 106 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 450 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 0.0770 chunk 53 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 277 ASN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.176854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.157770 restraints weight = 6113.610| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 1.68 r_work: 0.3869 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4853 Z= 0.169 Angle : 0.604 13.530 6563 Z= 0.294 Chirality : 0.040 0.269 760 Planarity : 0.003 0.043 819 Dihedral : 4.706 56.554 645 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.67 % Allowed : 23.17 % Favored : 72.15 % 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: -0.52 (0.36), residues: 583 helix: 0.94 (0.30), residues: 345 sheet: None (None), residues: 0 loop : -2.39 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 200 HIS 0.001 0.000 HIS B 359 PHE 0.011 0.001 PHE B 343 TYR 0.012 0.001 TYR A 412 ARG 0.002 0.000 ARG A 387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1434.86 seconds wall clock time: 26 minutes 35.06 seconds (1595.06 seconds total)