Starting phenix.real_space_refine on Tue Feb 13 14:32:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9l_25761/02_2024/7t9l_25761.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9l_25761/02_2024/7t9l_25761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9l_25761/02_2024/7t9l_25761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9l_25761/02_2024/7t9l_25761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9l_25761/02_2024/7t9l_25761.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9l_25761/02_2024/7t9l_25761.pdb" } resolution = 2.66 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= -0.001 sd= 0.016 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 37 5.16 5 C 4203 2.51 5 N 1084 2.21 5 O 1243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6567 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} 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: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 3.99, per 1000 atoms: 0.61 Number of scatterers: 6567 At special positions: 0 Unit cell: (78, 86, 122, 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 37 16.00 O 1243 8.00 N 1084 7.00 C 4203 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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=2.04 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 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.02 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 90 " " NAG D 703 " - " ASN D 103 " " NAG D 704 " - " ASN D 322 " " NAG D 705 " - " ASN D 432 " " NAG D 706 " - " ASN D 546 " Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.4 seconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 56.4% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.680A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.679A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 52 Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 4.206A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.622A pdb=" N SER D 155 " --> pdb=" O ILE D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 194 Proline residue: D 178 - end of helix removed outlier: 3.809A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 252 removed outlier: 4.532A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.767A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 319 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.500A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.721A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 397 through 413 removed outlier: 4.352A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA D 413 " --> pdb=" O SER D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.518A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.389A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.826A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.344A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 4.000A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 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 'D' and resid 262 through 263 removed outlier: 5.972A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.218A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 315 hydrogen bonds defined for protein. 906 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: 1.75 Time building geometry restraints manager: 2.57 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: 2050 1.34 - 1.46: 1710 1.46 - 1.58: 2934 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6752 Sorted by residual: bond pdb=" CG LEU D 558 " pdb=" CD1 LEU D 558 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.55e+00 bond pdb=" C1 NAG D 706 " pdb=" O5 NAG D 706 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.80e+00 bond pdb=" C1 NAG D 705 " pdb=" O5 NAG D 705 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.08e+00 bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.05e+00 bond pdb=" C1 NAG D 702 " pdb=" O5 NAG D 702 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.90e+00 ... (remaining 6747 not shown) Histogram of bond angle deviations from ideal: 98.28 - 105.50: 168 105.50 - 112.71: 3337 112.71 - 119.93: 2609 119.93 - 127.14: 2953 127.14 - 134.36: 109 Bond angle restraints: 9176 Sorted by residual: angle pdb=" CB LYS D 534 " pdb=" CG LYS D 534 " pdb=" CD LYS D 534 " ideal model delta sigma weight residual 111.30 121.60 -10.30 2.30e+00 1.89e-01 2.00e+01 angle pdb=" CB MET D 152 " pdb=" CG MET D 152 " pdb=" SD MET D 152 " ideal model delta sigma weight residual 112.70 125.97 -13.27 3.00e+00 1.11e-01 1.96e+01 angle pdb=" C SER A 359 " pdb=" N ASN A 360 " pdb=" CA ASN A 360 " ideal model delta sigma weight residual 122.46 128.55 -6.09 1.41e+00 5.03e-01 1.86e+01 angle pdb=" CB MET D 323 " pdb=" CG MET D 323 " pdb=" SD MET D 323 " ideal model delta sigma weight residual 112.70 125.10 -12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CB LYS D 600 " pdb=" CG LYS D 600 " pdb=" CD LYS D 600 " ideal model delta sigma weight residual 111.30 119.94 -8.64 2.30e+00 1.89e-01 1.41e+01 ... (remaining 9171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3669 17.94 - 35.89: 337 35.89 - 53.83: 57 53.83 - 71.78: 12 71.78 - 89.72: 6 Dihedral angle restraints: 4081 sinusoidal: 1740 harmonic: 2341 Sorted by residual: dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 38.00 55.00 1 1.00e+01 1.00e-02 4.09e+01 dihedral pdb=" CA GLN D 139 " pdb=" C GLN D 139 " pdb=" N GLU D 140 " pdb=" CA GLU D 140 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ALA D 396 " pdb=" C ALA D 396 " pdb=" N ASN D 397 " pdb=" CA ASN D 397 " ideal model delta harmonic sigma weight residual 180.00 159.15 20.85 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 4078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 644 0.048 - 0.095: 230 0.095 - 0.143: 85 0.143 - 0.191: 14 0.191 - 0.239: 7 Chirality restraints: 980 Sorted by residual: chirality pdb=" CG LEU D 267 " pdb=" CB LEU D 267 " pdb=" CD1 LEU D 267 " pdb=" CD2 LEU D 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB VAL D 581 " pdb=" CA VAL D 581 " pdb=" CG1 VAL D 581 " pdb=" CG2 VAL D 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE A 332 " pdb=" CA ILE A 332 " pdb=" CG1 ILE A 332 " pdb=" CG2 ILE A 332 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 977 not shown) Planarity restraints: 1186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 68 " 0.022 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C LYS D 68 " -0.077 2.00e-02 2.50e+03 pdb=" O LYS D 68 " 0.029 2.00e-02 2.50e+03 pdb=" N TRP D 69 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 241 " -0.017 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" C HIS D 241 " 0.058 2.00e-02 2.50e+03 pdb=" O HIS D 241 " -0.022 2.00e-02 2.50e+03 pdb=" N ALA D 242 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 240 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C LEU D 240 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU D 240 " -0.021 2.00e-02 2.50e+03 pdb=" N HIS D 241 " -0.019 2.00e-02 2.50e+03 ... (remaining 1183 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1755 2.80 - 3.33: 5984 3.33 - 3.85: 11578 3.85 - 4.38: 13246 4.38 - 4.90: 22673 Nonbonded interactions: 55236 Sorted by model distance: nonbonded pdb=" OH TYR D 183 " pdb=" OD1 ASP D 509 " model vdw 2.276 2.440 nonbonded pdb=" OH TYR D 217 " pdb=" OD2 ASP D 225 " model vdw 2.329 2.440 nonbonded pdb=" NZ LYS D 475 " pdb=" OE1 GLU D 495 " model vdw 2.333 2.520 nonbonded pdb=" OG SER D 170 " pdb=" NZ LYS D 174 " model vdw 2.341 2.520 nonbonded pdb=" NH1 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 2.360 2.520 ... (remaining 55231 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: 3.070 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: 13.370 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.150 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 0.006 0.078 6752 Z= 0.389 Angle : 0.956 13.272 9176 Z= 0.497 Chirality : 0.058 0.239 980 Planarity : 0.009 0.076 1179 Dihedral : 14.116 89.721 2559 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.14 % Allowed : 2.42 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.26), residues: 792 helix: -1.05 (0.22), residues: 393 sheet: 0.51 (0.73), residues: 44 loop : -1.02 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 594 HIS 0.009 0.002 HIS D 401 PHE 0.038 0.003 PHE A 347 TYR 0.029 0.002 TYR D 385 ARG 0.016 0.001 ARG D 582 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8386 (tp) cc_final: 0.8131 (tt) REVERT: D 110 GLU cc_start: 0.8260 (tp30) cc_final: 0.7953 (tp30) REVERT: D 114 LYS cc_start: 0.9112 (ttpp) cc_final: 0.8730 (tppt) REVERT: D 291 ILE cc_start: 0.8288 (mt) cc_final: 0.7977 (mm) REVERT: D 366 MET cc_start: 0.8645 (ttp) cc_final: 0.8381 (ttp) REVERT: D 435 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7390 (mm-30) REVERT: D 471 ASP cc_start: 0.8816 (p0) cc_final: 0.8580 (p0) REVERT: D 472 GLN cc_start: 0.8345 (mm110) cc_final: 0.7917 (mm-40) REVERT: D 579 MET cc_start: 0.8879 (mtm) cc_final: 0.8645 (ttm) REVERT: D 582 ARG cc_start: 0.8043 (mmm160) cc_final: 0.7712 (mmm160) outliers start: 1 outliers final: 1 residues processed: 185 average time/residue: 1.3650 time to fit residues: 264.3322 Evaluate side-chains 119 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN D 175 GLN D 374 HIS D 472 GLN ** D 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6752 Z= 0.272 Angle : 0.642 10.355 9176 Z= 0.327 Chirality : 0.045 0.168 980 Planarity : 0.005 0.038 1179 Dihedral : 6.512 115.282 1015 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.85 % Allowed : 14.81 % Favored : 82.34 % 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: 0.19 (0.29), residues: 792 helix: 0.59 (0.26), residues: 387 sheet: 0.11 (0.73), residues: 49 loop : -0.26 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 165 HIS 0.005 0.001 HIS D 241 PHE 0.021 0.002 PHE D 400 TYR 0.017 0.001 TYR D 41 ARG 0.008 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 114 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8372 (tp) cc_final: 0.8156 (tt) REVERT: D 114 LYS cc_start: 0.9167 (ttpp) cc_final: 0.8913 (tppt) REVERT: D 115 ARG cc_start: 0.7925 (tpm-80) cc_final: 0.7725 (tpt170) REVERT: D 123 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7443 (mtt) REVERT: D 297 MET cc_start: 0.9258 (mtm) cc_final: 0.8899 (mtp) REVERT: D 366 MET cc_start: 0.8581 (ttp) cc_final: 0.8347 (ttp) REVERT: D 579 MET cc_start: 0.9025 (mtm) cc_final: 0.8627 (ttm) outliers start: 20 outliers final: 9 residues processed: 122 average time/residue: 1.1200 time to fit residues: 144.0522 Evaluate side-chains 109 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 609 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 0.0030 chunk 71 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 134 ASN D 175 GLN ** D 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6752 Z= 0.297 Angle : 0.634 9.821 9176 Z= 0.323 Chirality : 0.045 0.237 980 Planarity : 0.004 0.038 1179 Dihedral : 5.155 54.873 1013 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.99 % Allowed : 16.38 % Favored : 79.63 % 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 (0.29), residues: 792 helix: 1.00 (0.26), residues: 395 sheet: 0.11 (0.71), residues: 49 loop : 0.04 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 165 HIS 0.004 0.001 HIS D 241 PHE 0.021 0.002 PHE D 400 TYR 0.017 0.001 TYR D 385 ARG 0.005 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 105 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8177 (pptt) REVERT: D 115 ARG cc_start: 0.8256 (tpm-80) cc_final: 0.7990 (tpm-80) REVERT: D 123 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7418 (mtt) REVERT: D 383 MET cc_start: 0.9051 (mtp) cc_final: 0.8806 (mtm) REVERT: D 579 MET cc_start: 0.9061 (mtm) cc_final: 0.8737 (ttm) outliers start: 28 outliers final: 10 residues processed: 119 average time/residue: 1.1630 time to fit residues: 145.9815 Evaluate side-chains 105 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 609 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 72 optimal weight: 0.1980 chunk 76 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 43 optimal weight: 0.0020 chunk 1 optimal weight: 0.0980 overall best weight: 0.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 GLN ** D 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6752 Z= 0.165 Angle : 0.595 10.852 9176 Z= 0.293 Chirality : 0.042 0.231 980 Planarity : 0.004 0.036 1179 Dihedral : 4.749 53.060 1013 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.70 % Allowed : 18.66 % Favored : 77.64 % 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: 1.04 (0.30), residues: 792 helix: 1.28 (0.26), residues: 396 sheet: 0.24 (0.74), residues: 49 loop : 0.20 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 69 HIS 0.003 0.001 HIS D 374 PHE 0.013 0.001 PHE D 369 TYR 0.012 0.001 TYR D 385 ARG 0.003 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 114 LYS cc_start: 0.8964 (mmpt) cc_final: 0.8609 (tppt) REVERT: D 115 ARG cc_start: 0.8252 (tpm-80) cc_final: 0.7890 (tpm-80) REVERT: D 297 MET cc_start: 0.9162 (mtm) cc_final: 0.8779 (mtp) REVERT: D 383 MET cc_start: 0.8989 (mtp) cc_final: 0.8779 (mtm) REVERT: D 440 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8558 (tp) REVERT: D 480 MET cc_start: 0.8717 (mtp) cc_final: 0.8506 (mtm) REVERT: D 497 TYR cc_start: 0.8162 (m-80) cc_final: 0.7517 (m-10) REVERT: D 579 MET cc_start: 0.9006 (mtm) cc_final: 0.8741 (ttm) REVERT: D 596 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8906 (mttm) outliers start: 26 outliers final: 5 residues processed: 109 average time/residue: 1.2976 time to fit residues: 148.6718 Evaluate side-chains 98 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 596 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.0050 chunk 44 optimal weight: 2.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6752 Z= 0.288 Angle : 0.628 10.492 9176 Z= 0.315 Chirality : 0.045 0.283 980 Planarity : 0.004 0.035 1179 Dihedral : 4.863 54.979 1013 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.42 % Allowed : 18.52 % Favored : 77.07 % 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: 1.21 (0.30), residues: 792 helix: 1.43 (0.26), residues: 398 sheet: 0.26 (0.72), residues: 49 loop : 0.28 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 165 HIS 0.004 0.001 HIS D 241 PHE 0.016 0.001 PHE D 400 TYR 0.016 0.001 TYR D 385 ARG 0.006 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 95 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7907 (tpm-80) REVERT: D 123 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7591 (mtt) REVERT: D 291 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7860 (tp) REVERT: D 297 MET cc_start: 0.9258 (mtm) cc_final: 0.8846 (mtp) REVERT: D 383 MET cc_start: 0.9061 (mtp) cc_final: 0.8853 (mtm) REVERT: D 579 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8719 (ttm) REVERT: D 596 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8893 (mttm) outliers start: 31 outliers final: 12 residues processed: 116 average time/residue: 1.1215 time to fit residues: 137.6823 Evaluate side-chains 110 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 596 LYS Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 609 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 55 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN D 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6752 Z= 0.245 Angle : 0.618 10.960 9176 Z= 0.308 Chirality : 0.044 0.295 980 Planarity : 0.004 0.034 1179 Dihedral : 4.797 54.350 1013 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.56 % Allowed : 19.23 % Favored : 77.21 % 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: 1.32 (0.30), residues: 792 helix: 1.50 (0.26), residues: 397 sheet: 0.22 (0.72), residues: 49 loop : 0.38 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 165 HIS 0.003 0.001 HIS D 241 PHE 0.014 0.001 PHE D 369 TYR 0.015 0.001 TYR D 385 ARG 0.005 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 95 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 114 LYS cc_start: 0.8918 (mmpt) cc_final: 0.8614 (tppt) REVERT: D 115 ARG cc_start: 0.8295 (tpm-80) cc_final: 0.7926 (tpm-80) REVERT: D 123 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7533 (mtt) REVERT: D 234 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8775 (ttpt) REVERT: D 291 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7867 (tp) REVERT: D 297 MET cc_start: 0.9255 (mtm) cc_final: 0.8691 (mtp) REVERT: D 440 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8634 (tp) REVERT: D 497 TYR cc_start: 0.7955 (m-80) cc_final: 0.7568 (m-10) REVERT: D 579 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8720 (ttm) REVERT: D 596 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8905 (mttm) outliers start: 25 outliers final: 14 residues processed: 113 average time/residue: 1.2366 time to fit residues: 147.9215 Evaluate side-chains 109 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 596 LYS Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 609 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 46 optimal weight: 0.0370 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 14 optimal weight: 0.2980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6752 Z= 0.193 Angle : 0.604 11.404 9176 Z= 0.300 Chirality : 0.043 0.300 980 Planarity : 0.003 0.034 1179 Dihedral : 4.600 53.814 1013 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.70 % Allowed : 19.80 % Favored : 76.50 % 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 (0.30), residues: 792 helix: 1.59 (0.26), residues: 395 sheet: -0.22 (0.64), residues: 59 loop : 0.50 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 165 HIS 0.003 0.001 HIS D 374 PHE 0.014 0.001 PHE D 369 TYR 0.012 0.001 TYR D 385 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 114 LYS cc_start: 0.8976 (mmpt) cc_final: 0.8625 (tppt) REVERT: D 115 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.8037 (tpm-80) REVERT: D 123 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7766 (mtt) REVERT: D 179 LEU cc_start: 0.9008 (mm) cc_final: 0.8620 (tp) REVERT: D 234 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8758 (ttpt) REVERT: D 291 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7855 (tp) REVERT: D 297 MET cc_start: 0.9267 (mtm) cc_final: 0.8710 (mtp) REVERT: D 497 TYR cc_start: 0.7963 (m-80) cc_final: 0.7601 (m-10) REVERT: D 579 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8733 (ttm) REVERT: D 596 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8919 (mttm) outliers start: 26 outliers final: 10 residues processed: 114 average time/residue: 0.9705 time to fit residues: 117.6944 Evaluate side-chains 108 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 596 LYS Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 609 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN D 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6752 Z= 0.277 Angle : 0.661 12.757 9176 Z= 0.328 Chirality : 0.045 0.338 980 Planarity : 0.004 0.033 1179 Dihedral : 4.732 54.761 1013 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.56 % Allowed : 20.37 % Favored : 76.07 % 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: 1.31 (0.30), residues: 792 helix: 1.53 (0.26), residues: 399 sheet: 0.01 (0.73), residues: 49 loop : 0.35 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 594 HIS 0.004 0.001 HIS D 241 PHE 0.014 0.001 PHE D 369 TYR 0.014 0.001 TYR D 385 ARG 0.007 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: D 55 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7588 (p) REVERT: D 115 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8041 (tpm-80) REVERT: D 123 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7507 (mtt) REVERT: D 234 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8776 (ttpt) REVERT: D 291 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7839 (tp) REVERT: D 497 TYR cc_start: 0.8211 (m-80) cc_final: 0.7815 (m-10) REVERT: D 579 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8749 (ttm) REVERT: D 596 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.8912 (mttm) outliers start: 25 outliers final: 12 residues processed: 108 average time/residue: 1.0046 time to fit residues: 115.3605 Evaluate side-chains 106 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 596 LYS Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 609 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.0770 chunk 52 optimal weight: 0.3980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 154 ASN D 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6752 Z= 0.207 Angle : 0.647 13.555 9176 Z= 0.322 Chirality : 0.044 0.333 980 Planarity : 0.004 0.033 1179 Dihedral : 4.601 53.847 1013 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.99 % Allowed : 21.37 % Favored : 75.64 % 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: 1.39 (0.30), residues: 792 helix: 1.64 (0.26), residues: 391 sheet: -0.35 (0.65), residues: 59 loop : 0.47 (0.36), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 594 HIS 0.003 0.001 HIS D 374 PHE 0.014 0.001 PHE D 369 TYR 0.011 0.001 TYR D 385 ARG 0.007 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: D 55 THR cc_start: 0.7895 (OUTLIER) cc_final: 0.7506 (p) REVERT: D 115 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8032 (tpm-80) REVERT: D 123 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7593 (mtt) REVERT: D 234 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8768 (ttpt) REVERT: D 291 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7806 (tp) REVERT: D 297 MET cc_start: 0.9192 (mtm) cc_final: 0.8803 (mtp) REVERT: D 479 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7170 (mt-10) REVERT: D 497 TYR cc_start: 0.8120 (m-80) cc_final: 0.7733 (m-80) REVERT: D 579 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8736 (ttm) REVERT: D 596 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8916 (mttm) outliers start: 21 outliers final: 11 residues processed: 110 average time/residue: 1.0163 time to fit residues: 118.7774 Evaluate side-chains 107 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 596 LYS Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 609 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 49 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 19 optimal weight: 0.0980 chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6752 Z= 0.209 Angle : 0.661 17.012 9176 Z= 0.330 Chirality : 0.044 0.340 980 Planarity : 0.004 0.033 1179 Dihedral : 4.595 54.116 1013 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.71 % Allowed : 22.08 % Favored : 75.21 % 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: 1.41 (0.30), residues: 792 helix: 1.65 (0.26), residues: 391 sheet: -0.02 (0.66), residues: 53 loop : 0.39 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 165 HIS 0.003 0.001 HIS D 374 PHE 0.020 0.001 PHE A 374 TYR 0.011 0.001 TYR D 385 ARG 0.007 0.000 ARG A 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 55 THR cc_start: 0.7814 (OUTLIER) cc_final: 0.7417 (p) REVERT: D 114 LYS cc_start: 0.8920 (mmmt) cc_final: 0.8513 (mmtm) REVERT: D 115 ARG cc_start: 0.8322 (tpm-80) cc_final: 0.8057 (tpm-80) REVERT: D 123 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7787 (mtt) REVERT: D 152 MET cc_start: 0.8541 (tpp) cc_final: 0.8287 (mmm) REVERT: D 169 ARG cc_start: 0.8501 (ttm-80) cc_final: 0.7656 (ttm110) REVERT: D 179 LEU cc_start: 0.9034 (mm) cc_final: 0.8675 (tp) REVERT: D 234 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8767 (ttpt) REVERT: D 291 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7817 (tp) REVERT: D 297 MET cc_start: 0.9157 (mtm) cc_final: 0.8736 (mtp) REVERT: D 479 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7110 (mt-10) REVERT: D 497 TYR cc_start: 0.8224 (m-80) cc_final: 0.7726 (m-80) REVERT: D 518 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8198 (ttp80) REVERT: D 579 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8740 (ttm) REVERT: D 596 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8907 (mttm) outliers start: 19 outliers final: 10 residues processed: 112 average time/residue: 1.0758 time to fit residues: 127.6222 Evaluate side-chains 108 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 518 ARG Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 596 LYS Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 609 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.0980 chunk 62 optimal weight: 0.3980 chunk 26 optimal weight: 0.0980 chunk 64 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.105616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.079837 restraints weight = 11901.576| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.79 r_work: 0.2985 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6752 Z= 0.201 Angle : 0.659 16.076 9176 Z= 0.328 Chirality : 0.044 0.334 980 Planarity : 0.004 0.033 1179 Dihedral : 4.562 53.977 1013 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.28 % Allowed : 22.93 % Favored : 74.79 % 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: 1.41 (0.30), residues: 792 helix: 1.67 (0.26), residues: 391 sheet: 0.00 (0.66), residues: 53 loop : 0.37 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 165 HIS 0.003 0.001 HIS D 374 PHE 0.014 0.001 PHE D 369 TYR 0.011 0.001 TYR D 385 ARG 0.006 0.000 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3094.37 seconds wall clock time: 55 minutes 43.85 seconds (3343.85 seconds total)