Starting phenix.real_space_refine on Fri Dec 27 20:08:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aqs_15588/12_2024/8aqs_15588.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aqs_15588/12_2024/8aqs_15588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8aqs_15588/12_2024/8aqs_15588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aqs_15588/12_2024/8aqs_15588.map" model { file = "/net/cci-nas-00/data/ceres_data/8aqs_15588/12_2024/8aqs_15588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aqs_15588/12_2024/8aqs_15588.cif" } resolution = 2.92 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= 0.030 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 Zn 1 6.06 5 S 37 5.16 5 C 4155 2.51 5 N 1073 2.21 5 O 1227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6493 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1543 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 11, 'TRANS': 181} Chain: "B" Number of atoms: 4864 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Conformer: "C" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} bond proxies already assigned to first conformer: 4985 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 72 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6, 'water': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.48, per 1000 atoms: 1.00 Number of scatterers: 6493 At special positions: 0 Unit cell: (89.2672, 78.1088, 118.685, 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) Zn 1 29.99 S 37 16.00 O 1227 8.00 N 1073 7.00 C 4155 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG B 901 " - " ASN B 53 " " NAG B 902 " - " ASN B 90 " " NAG B 903 " - " ASN B 103 " " NAG B 904 " - " ASN B 546 " " NAG B 905 " - " ASN B 322 " Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 906 " pdb="ZN ZN B 906 " - pdb=" NE2 HIS B 374 " pdb="ZN ZN B 906 " - pdb=" NE2 HIS B 378 " 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 5 sheets defined 53.7% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.105A pdb=" N PHE A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.662A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.902A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 53 removed outlier: 3.945A pdb=" N TYR B 41 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN B 42 " --> pdb=" O ASP B 38 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 81 Processing helix chain 'B' and resid 90 through 101 Processing helix chain 'B' and resid 109 through 130 Processing helix chain 'B' and resid 147 through 154 Processing helix chain 'B' and resid 157 through 194 removed outlier: 3.663A pdb=" N ARG B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG B 169 " --> pdb=" O TRP B 165 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLN B 175 " --> pdb=" O GLU B 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 176 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Proline residue: B 178 - end of helix Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 220 through 252 removed outlier: 4.068A pdb=" N GLU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 232 " --> pdb=" O HIS B 228 " (cutoff:3.500A) Proline residue: B 235 - end of helix Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 275 through 279 removed outlier: 3.739A pdb=" N TYR B 279 " --> pdb=" O THR B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 300 Processing helix chain 'B' and resid 303 through 311 removed outlier: 3.599A pdb=" N ALA B 311 " --> pdb=" O ILE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 319 removed outlier: 3.505A pdb=" N VAL B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 331 removed outlier: 4.166A pdb=" N TRP B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 385 removed outlier: 3.889A pdb=" N PHE B 369 " --> pdb=" O THR B 365 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 370 " --> pdb=" O MET B 366 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR B 385 " --> pdb=" O TYR B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 393 removed outlier: 3.528A pdb=" N ARG B 393 " --> pdb=" O PHE B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 412 removed outlier: 3.664A pdb=" N SER B 411 " --> pdb=" O ILE B 407 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA B 412 " --> pdb=" O MET B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 421 Processing helix chain 'B' and resid 431 through 444 removed outlier: 3.903A pdb=" N ILE B 436 " --> pdb=" O ASN B 432 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 466 Processing helix chain 'B' and resid 469 through 471 No H-bonds generated for 'chain 'B' and resid 469 through 471' Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.654A pdb=" N ARG B 482 " --> pdb=" O TRP B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 503 through 508 removed outlier: 3.590A pdb=" N SER B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 533 removed outlier: 3.645A pdb=" N THR B 517 " --> pdb=" O ILE B 513 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR B 519 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 547 through 559 removed outlier: 3.980A pdb=" N GLY B 551 " --> pdb=" O SER B 547 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 574 Processing helix chain 'B' and resid 581 through 599 Proline residue: B 590 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'B' and resid 262 through 263 removed outlier: 6.112A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 347 through 352 removed outlier: 6.053A pdb=" N ASP B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) 292 hydrogen bonds defined for protein. 818 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: 1.99 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: 2074 1.34 - 1.46: 1675 1.46 - 1.58: 2869 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6676 Sorted by residual: bond pdb=" C1 NAG B 902 " pdb=" O5 NAG B 902 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.06e+00 bond pdb=" C1 NAG B 904 " pdb=" O5 NAG B 904 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" C1 NAG B 903 " pdb=" O5 NAG B 903 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.66e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.40e+00 ... (remaining 6671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 8959 2.07 - 4.13: 102 4.13 - 6.20: 13 6.20 - 8.26: 1 8.26 - 10.33: 1 Bond angle restraints: 9076 Sorted by residual: angle pdb=" C PHE A 371 " pdb=" N ALA A 372 " pdb=" CA ALA A 372 " ideal model delta sigma weight residual 121.80 132.13 -10.33 2.44e+00 1.68e-01 1.79e+01 angle pdb=" C PRO B 84 " pdb=" N LEU B 85 " pdb=" CA LEU B 85 " ideal model delta sigma weight residual 121.54 127.71 -6.17 1.91e+00 2.74e-01 1.04e+01 angle pdb=" N ILE A 418 " pdb=" CA ILE A 418 " pdb=" C ILE A 418 " ideal model delta sigma weight residual 111.81 109.22 2.59 8.60e-01 1.35e+00 9.08e+00 angle pdb=" N LYS B 174 " pdb=" CA LYS B 174 " pdb=" C LYS B 174 " ideal model delta sigma weight residual 112.72 109.37 3.35 1.14e+00 7.69e-01 8.64e+00 angle pdb=" N GLN B 175 " pdb=" CA GLN B 175 " pdb=" C GLN B 175 " ideal model delta sigma weight residual 114.64 110.19 4.45 1.52e+00 4.33e-01 8.55e+00 ... (remaining 9071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.81: 3737 21.81 - 43.62: 229 43.62 - 65.43: 25 65.43 - 87.24: 9 87.24 - 109.05: 8 Dihedral angle restraints: 4008 sinusoidal: 1689 harmonic: 2319 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 127.82 -34.82 1 1.00e+01 1.00e-02 1.72e+01 dihedral pdb=" C1 NAG B 905 " pdb=" C2 NAG B 905 " pdb=" C3 NAG B 905 " pdb=" O3 NAG B 905 " ideal model delta sinusoidal sigma weight residual -175.09 -66.04 -109.05 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" C1 NAG B 905 " pdb=" C2 NAG B 905 " pdb=" C3 NAG B 905 " pdb=" C4 NAG B 905 " ideal model delta sinusoidal sigma weight residual -52.39 55.85 -108.24 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 4005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 897 0.081 - 0.163: 66 0.163 - 0.244: 0 0.244 - 0.325: 0 0.325 - 0.406: 1 Chirality restraints: 964 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" CB ILE B 407 " pdb=" CA ILE B 407 " pdb=" CG1 ILE B 407 " pdb=" CG2 ILE B 407 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" C1 NAG B 904 " pdb=" ND2 ASN B 546 " pdb=" C2 NAG B 904 " pdb=" O5 NAG B 904 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 961 not shown) Planarity restraints: 1176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 145 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO B 146 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 234 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.35e+00 pdb=" N PRO B 235 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 235 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 235 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 293 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.64e+00 pdb=" C VAL B 293 " 0.022 2.00e-02 2.50e+03 pdb=" O VAL B 293 " -0.008 2.00e-02 2.50e+03 pdb=" N THR B 294 " -0.008 2.00e-02 2.50e+03 ... (remaining 1173 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 996 2.76 - 3.30: 5887 3.30 - 3.83: 10338 3.83 - 4.37: 12079 4.37 - 4.90: 21510 Nonbonded interactions: 50810 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" O ILE B 358 " model vdw 2.227 3.040 nonbonded pdb=" NE ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 2.250 3.120 nonbonded pdb=" NH2 ARG A 454 " pdb=" O SER A 469 " model vdw 2.307 3.120 nonbonded pdb=" OG SER A 438 " pdb=" OD2 ASP A 442 " model vdw 2.337 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.369 3.040 ... (remaining 50805 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 ========== 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=0.40 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: 2.270 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 23.490 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:18.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 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 0.030 6676 Z= 0.172 Angle : 0.543 10.326 9076 Z= 0.292 Chirality : 0.043 0.406 964 Planarity : 0.004 0.055 1170 Dihedral : 14.740 109.048 2508 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.93 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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 (0.31), residues: 785 helix: 1.81 (0.29), residues: 357 sheet: 1.33 (0.79), residues: 45 loop : -0.97 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 477 HIS 0.003 0.001 HIS B 374 PHE 0.018 0.001 PHE B 400 TYR 0.020 0.001 TYR A 501 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.751 Fit side-chains REVERT: A 440 LYS cc_start: 0.8615 (mttm) cc_final: 0.8305 (mmtm) REVERT: A 444 LYS cc_start: 0.8513 (mtpt) cc_final: 0.8226 (mtpm) REVERT: A 467 ASP cc_start: 0.8491 (t0) cc_final: 0.8133 (t0) REVERT: B 60 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7522 (mm-40) REVERT: B 89 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8120 (mm-40) REVERT: B 102 GLN cc_start: 0.7907 (pt0) cc_final: 0.7402 (mm110) REVERT: B 131 LYS cc_start: 0.7573 (ptmm) cc_final: 0.7283 (tttm) REVERT: B 150 GLU cc_start: 0.7073 (tp30) cc_final: 0.6606 (mp0) REVERT: B 190 MET cc_start: 0.7201 (tmm) cc_final: 0.6979 (tmm) REVERT: B 213 ASP cc_start: 0.6790 (p0) cc_final: 0.6510 (t0) REVERT: B 270 MET cc_start: 0.6371 (tpp) cc_final: 0.6046 (mmm) REVERT: B 397 ASN cc_start: 0.8226 (p0) cc_final: 0.7972 (p0) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 1.1957 time to fit residues: 142.3795 Evaluate side-chains 81 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 5.9990 chunk 59 optimal weight: 0.0060 chunk 32 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN B 34 HIS C B 325 GLN B 401 HIS B 472 GLN B 552 GLN B 598 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6676 Z= 0.294 Angle : 0.625 10.126 9076 Z= 0.322 Chirality : 0.046 0.383 964 Planarity : 0.005 0.049 1170 Dihedral : 8.351 75.618 985 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.83 % Favored : 95.92 % Rotamer: Outliers : 1.44 % Allowed : 9.67 % Favored : 88.89 % 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: 0.44 (0.30), residues: 785 helix: 1.40 (0.28), residues: 370 sheet: 0.81 (0.69), residues: 55 loop : -0.99 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.005 0.001 HIS B 374 PHE 0.035 0.002 PHE B 400 TYR 0.026 0.002 TYR B 183 ARG 0.007 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.757 Fit side-chains REVERT: A 420 ASP cc_start: 0.9065 (m-30) cc_final: 0.8862 (m-30) REVERT: A 440 LYS cc_start: 0.8608 (mttm) cc_final: 0.8268 (mmtm) REVERT: A 444 LYS cc_start: 0.8448 (mtpt) cc_final: 0.8152 (mtpm) REVERT: B 131 LYS cc_start: 0.7410 (ptmm) cc_final: 0.7181 (tttm) REVERT: B 150 GLU cc_start: 0.6904 (tp30) cc_final: 0.6471 (mp0) REVERT: B 213 ASP cc_start: 0.6957 (p0) cc_final: 0.6698 (t0) REVERT: B 287 GLN cc_start: 0.7295 (mm-40) cc_final: 0.6958 (pp30) outliers start: 10 outliers final: 3 residues processed: 96 average time/residue: 1.2189 time to fit residues: 123.3300 Evaluate side-chains 87 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 530 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 70 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN B 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6676 Z= 0.248 Angle : 0.608 10.170 9076 Z= 0.308 Chirality : 0.045 0.390 964 Planarity : 0.004 0.049 1170 Dihedral : 6.964 55.338 985 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.95 % Favored : 95.79 % Rotamer: Outliers : 1.73 % Allowed : 11.54 % Favored : 86.72 % 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: 0.42 (0.30), residues: 785 helix: 1.44 (0.28), residues: 364 sheet: 0.72 (0.68), residues: 55 loop : -1.01 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 477 HIS 0.004 0.001 HIS B 374 PHE 0.026 0.002 PHE B 400 TYR 0.023 0.002 TYR B 183 ARG 0.007 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.705 Fit side-chains REVERT: A 346 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7252 (ptm160) REVERT: A 440 LYS cc_start: 0.8675 (mttm) cc_final: 0.8294 (mmtm) REVERT: A 444 LYS cc_start: 0.8475 (mtpt) cc_final: 0.8258 (mtpm) REVERT: B 287 GLN cc_start: 0.7367 (mm-40) cc_final: 0.6944 (pp30) outliers start: 12 outliers final: 6 residues processed: 93 average time/residue: 1.2171 time to fit residues: 119.7571 Evaluate side-chains 84 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 530 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN B 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6676 Z= 0.220 Angle : 0.586 10.205 9076 Z= 0.295 Chirality : 0.044 0.392 964 Planarity : 0.004 0.050 1170 Dihedral : 6.303 55.296 985 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.21 % Favored : 95.54 % Rotamer: Outliers : 2.02 % Allowed : 12.41 % Favored : 85.57 % 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: 0.47 (0.30), residues: 785 helix: 1.48 (0.28), residues: 364 sheet: 0.77 (0.68), residues: 55 loop : -0.98 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 477 HIS 0.004 0.001 HIS B 374 PHE 0.023 0.001 PHE B 400 TYR 0.019 0.002 TYR B 50 ARG 0.006 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.688 Fit side-chains REVERT: A 346 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7268 (ptm160) REVERT: A 440 LYS cc_start: 0.8658 (mttm) cc_final: 0.8301 (mmtm) REVERT: A 444 LYS cc_start: 0.8487 (mtpt) cc_final: 0.8268 (mtpm) REVERT: B 287 GLN cc_start: 0.7329 (mm-40) cc_final: 0.7043 (pp30) REVERT: B 341 LYS cc_start: 0.7726 (mmmt) cc_final: 0.7129 (mmmt) outliers start: 14 outliers final: 9 residues processed: 91 average time/residue: 1.1573 time to fit residues: 111.3986 Evaluate side-chains 86 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 530 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.0970 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN B 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6676 Z= 0.190 Angle : 0.566 10.275 9076 Z= 0.284 Chirality : 0.043 0.389 964 Planarity : 0.004 0.049 1170 Dihedral : 5.814 54.720 985 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.57 % Favored : 96.17 % Rotamer: Outliers : 2.02 % Allowed : 13.71 % Favored : 84.27 % 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: 0.56 (0.30), residues: 785 helix: 1.57 (0.28), residues: 364 sheet: 0.75 (0.68), residues: 55 loop : -0.94 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 477 HIS 0.004 0.001 HIS B 374 PHE 0.016 0.001 PHE B 400 TYR 0.016 0.001 TYR A 501 ARG 0.008 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7267 (ptm160) REVERT: A 440 LYS cc_start: 0.8649 (mttm) cc_final: 0.8301 (mmtm) REVERT: A 444 LYS cc_start: 0.8474 (mtpt) cc_final: 0.8264 (mtpm) REVERT: B 287 GLN cc_start: 0.7374 (mm-40) cc_final: 0.7069 (pp30) REVERT: B 341 LYS cc_start: 0.7736 (mmmt) cc_final: 0.7139 (mmmt) outliers start: 14 outliers final: 9 residues processed: 88 average time/residue: 1.1777 time to fit residues: 109.4890 Evaluate side-chains 83 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 530 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 HIS B 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6676 Z= 0.210 Angle : 0.575 10.236 9076 Z= 0.289 Chirality : 0.044 0.391 964 Planarity : 0.004 0.048 1170 Dihedral : 5.631 55.349 985 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.21 % Favored : 95.54 % Rotamer: Outliers : 2.31 % Allowed : 14.00 % Favored : 83.69 % 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: 0.57 (0.30), residues: 785 helix: 1.57 (0.27), residues: 364 sheet: 0.78 (0.68), residues: 55 loop : -0.93 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 477 HIS 0.005 0.001 HIS B 228 PHE 0.019 0.001 PHE B 400 TYR 0.018 0.001 TYR B 50 ARG 0.008 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7256 (ptm160) REVERT: A 440 LYS cc_start: 0.8679 (mttm) cc_final: 0.8326 (mmtm) REVERT: A 444 LYS cc_start: 0.8472 (mtpt) cc_final: 0.8263 (mtpm) REVERT: B 287 GLN cc_start: 0.7318 (mm-40) cc_final: 0.7031 (pp30) REVERT: B 341 LYS cc_start: 0.7746 (mmmt) cc_final: 0.7105 (mmmt) outliers start: 16 outliers final: 10 residues processed: 88 average time/residue: 1.2588 time to fit residues: 116.7454 Evaluate side-chains 84 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 530 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 47 optimal weight: 0.0050 chunk 45 optimal weight: 0.0040 chunk 34 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 30 optimal weight: 0.0470 chunk 44 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN B 228 HIS B 325 GLN B 472 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6676 Z= 0.148 Angle : 0.528 10.384 9076 Z= 0.263 Chirality : 0.042 0.379 964 Planarity : 0.004 0.047 1170 Dihedral : 5.081 53.774 985 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.06 % Favored : 96.68 % Rotamer: Outliers : 2.16 % Allowed : 14.57 % Favored : 83.26 % 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: 0.84 (0.31), residues: 785 helix: 1.85 (0.28), residues: 362 sheet: 0.69 (0.67), residues: 55 loop : -0.80 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 477 HIS 0.009 0.001 HIS B 228 PHE 0.010 0.001 PHE B 504 TYR 0.012 0.001 TYR A 501 ARG 0.009 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.676 Fit side-chains REVERT: A 346 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7345 (ptm160) REVERT: A 440 LYS cc_start: 0.8639 (mttm) cc_final: 0.8305 (mmtm) REVERT: A 444 LYS cc_start: 0.8511 (mtpt) cc_final: 0.8249 (mtpm) REVERT: B 102 GLN cc_start: 0.8007 (pt0) cc_final: 0.7395 (mm110) REVERT: B 287 GLN cc_start: 0.7357 (mm-40) cc_final: 0.7056 (pp30) REVERT: B 341 LYS cc_start: 0.7717 (mmmt) cc_final: 0.7132 (mmmt) outliers start: 15 outliers final: 8 residues processed: 95 average time/residue: 1.1155 time to fit residues: 112.2466 Evaluate side-chains 85 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 530 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 0.0870 chunk 37 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 68 optimal weight: 0.3980 chunk 72 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 HIS B 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6676 Z= 0.165 Angle : 0.535 10.294 9076 Z= 0.269 Chirality : 0.043 0.375 964 Planarity : 0.004 0.047 1170 Dihedral : 5.074 54.624 985 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.70 % Favored : 96.05 % Rotamer: Outliers : 1.73 % Allowed : 16.02 % Favored : 82.25 % 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: 0.81 (0.31), residues: 785 helix: 1.84 (0.28), residues: 365 sheet: 0.68 (0.67), residues: 55 loop : -0.86 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 477 HIS 0.009 0.001 HIS B 228 PHE 0.013 0.001 PHE B 400 TYR 0.011 0.001 TYR B 516 ARG 0.009 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7341 (ptm160) REVERT: A 440 LYS cc_start: 0.8653 (mttm) cc_final: 0.8310 (mmtm) REVERT: A 444 LYS cc_start: 0.8511 (mtpt) cc_final: 0.8245 (mtpm) REVERT: B 102 GLN cc_start: 0.7994 (pt0) cc_final: 0.7352 (mm110) REVERT: B 287 GLN cc_start: 0.7359 (mm-40) cc_final: 0.7058 (pp30) REVERT: B 341 LYS cc_start: 0.7722 (mmmt) cc_final: 0.7134 (mmmt) outliers start: 12 outliers final: 9 residues processed: 86 average time/residue: 1.3592 time to fit residues: 123.2560 Evaluate side-chains 87 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 530 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 0.0470 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6676 Z= 0.175 Angle : 0.541 10.283 9076 Z= 0.272 Chirality : 0.043 0.375 964 Planarity : 0.004 0.047 1170 Dihedral : 5.032 54.965 985 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.06 % Favored : 96.68 % Rotamer: Outliers : 1.59 % Allowed : 16.16 % Favored : 82.25 % 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: 0.82 (0.31), residues: 785 helix: 1.83 (0.28), residues: 365 sheet: 0.68 (0.67), residues: 55 loop : -0.82 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 477 HIS 0.004 0.001 HIS B 374 PHE 0.013 0.001 PHE B 400 TYR 0.012 0.001 TYR B 183 ARG 0.009 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7342 (ptm160) REVERT: A 440 LYS cc_start: 0.8664 (mttm) cc_final: 0.8318 (mmtm) REVERT: A 444 LYS cc_start: 0.8512 (mtpt) cc_final: 0.8243 (mtpm) REVERT: B 102 GLN cc_start: 0.7985 (pt0) cc_final: 0.7357 (mm110) REVERT: B 287 GLN cc_start: 0.7362 (mm-40) cc_final: 0.7059 (pp30) REVERT: B 341 LYS cc_start: 0.7727 (mmmt) cc_final: 0.7141 (mmmt) outliers start: 11 outliers final: 9 residues processed: 86 average time/residue: 1.2221 time to fit residues: 111.2016 Evaluate side-chains 88 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 530 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 0.0050 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 0.0570 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 overall best weight: 0.7516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 HIS B 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6676 Z= 0.191 Angle : 0.551 10.244 9076 Z= 0.279 Chirality : 0.043 0.376 964 Planarity : 0.004 0.046 1170 Dihedral : 5.061 55.365 985 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.70 % Favored : 96.05 % Rotamer: Outliers : 1.44 % Allowed : 16.45 % Favored : 82.11 % 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: 0.80 (0.31), residues: 785 helix: 1.80 (0.28), residues: 365 sheet: 0.68 (0.67), residues: 55 loop : -0.83 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 477 HIS 0.012 0.001 HIS B 228 PHE 0.016 0.001 PHE B 400 TYR 0.012 0.001 TYR B 385 ARG 0.009 0.000 ARG A 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7337 (ptm160) REVERT: A 440 LYS cc_start: 0.8673 (mttm) cc_final: 0.8320 (mmtm) REVERT: A 444 LYS cc_start: 0.8499 (mtpt) cc_final: 0.8229 (mtpm) REVERT: B 102 GLN cc_start: 0.7981 (pt0) cc_final: 0.7376 (mm110) REVERT: B 287 GLN cc_start: 0.7322 (mm-40) cc_final: 0.7037 (pp30) REVERT: B 341 LYS cc_start: 0.7786 (mmmt) cc_final: 0.7077 (mmmt) outliers start: 10 outliers final: 8 residues processed: 82 average time/residue: 1.2724 time to fit residues: 109.9161 Evaluate side-chains 84 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 530 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 0.0020 chunk 25 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 HIS B 472 GLN B 505 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.157609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.114675 restraints weight = 15439.222| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.96 r_work: 0.3094 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6676 Z= 0.189 Angle : 0.557 10.252 9076 Z= 0.282 Chirality : 0.043 0.376 964 Planarity : 0.004 0.047 1170 Dihedral : 5.051 55.235 985 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.44 % Favored : 96.30 % Rotamer: Outliers : 1.30 % Allowed : 16.16 % Favored : 82.54 % 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: 0.79 (0.31), residues: 785 helix: 1.79 (0.28), residues: 365 sheet: 0.70 (0.67), residues: 55 loop : -0.84 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 477 HIS 0.014 0.001 HIS B 228 PHE 0.015 0.001 PHE B 400 TYR 0.018 0.001 TYR B 50 ARG 0.009 0.000 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2746.51 seconds wall clock time: 50 minutes 22.89 seconds (3022.89 seconds total)