Starting phenix.real_space_refine on Wed Jan 17 21:47:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm6_27528/01_2024/8dm6_27528.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm6_27528/01_2024/8dm6_27528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm6_27528/01_2024/8dm6_27528.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm6_27528/01_2024/8dm6_27528.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm6_27528/01_2024/8dm6_27528.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm6_27528/01_2024/8dm6_27528.pdb" } resolution = 2.77 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 4200 2.51 5 N 1082 2.21 5 O 1240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6559 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1604 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: 4.05, per 1000 atoms: 0.62 Number of scatterers: 6559 At special positions: 0 Unit cell: (79, 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 1240 8.00 N 1082 7.00 C 4200 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 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: 2.25 Conformation dependent library (CDL) restraints added in 1.2 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: 1500 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 57.3% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.866A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.572A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.284A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'D' and resid 20 through 53 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: 4.166A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.620A 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: 3.609A 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: 3.807A 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: 4.500A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.896A 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: 3.824A 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 318 Processing helix chain 'D' and resid 324 through 331 Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.744A 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: 4.340A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.531A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.335A 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: 3.747A 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: 4.372A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.648A 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: 3.992A 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 removed outlier: 6.539A pdb=" N ALA A 435 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.976A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.246A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 343 hydrogen bonds defined for protein. 984 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: 1.68 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2084 1.35 - 1.48: 1851 1.48 - 1.61: 2752 1.61 - 1.73: 0 1.73 - 1.86: 58 Bond restraints: 6745 Sorted by residual: bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.50e+00 bond pdb=" C1 NAG D 706 " pdb=" O5 NAG D 706 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.52e+00 bond pdb=" CG PRO A 330 " pdb=" CD PRO A 330 " ideal model delta sigma weight residual 1.503 1.575 -0.072 3.40e-02 8.65e+02 4.47e+00 bond pdb=" C1 NAG D 704 " pdb=" O5 NAG D 704 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" C1 NAG D 702 " pdb=" O5 NAG D 702 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.52e+00 ... (remaining 6740 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.57: 171 105.57 - 112.75: 3358 112.75 - 119.93: 2510 119.93 - 127.11: 3013 127.11 - 134.29: 114 Bond angle restraints: 9166 Sorted by residual: angle pdb=" N ALA A 372 " pdb=" CA ALA A 372 " pdb=" C ALA A 372 " ideal model delta sigma weight residual 109.81 120.82 -11.01 2.21e+00 2.05e-01 2.48e+01 angle pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " ideal model delta sigma weight residual 114.40 125.13 -10.73 2.30e+00 1.89e-01 2.18e+01 angle pdb=" CB MET D 152 " pdb=" CG MET D 152 " pdb=" SD MET D 152 " ideal model delta sigma weight residual 112.70 124.88 -12.18 3.00e+00 1.11e-01 1.65e+01 angle pdb=" CB LYS D 534 " pdb=" CG LYS D 534 " pdb=" CD LYS D 534 " ideal model delta sigma weight residual 111.30 120.35 -9.05 2.30e+00 1.89e-01 1.55e+01 angle pdb=" CA PRO A 330 " pdb=" N PRO A 330 " pdb=" CD PRO A 330 " ideal model delta sigma weight residual 112.00 106.58 5.42 1.40e+00 5.10e-01 1.50e+01 ... (remaining 9161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 3648 17.48 - 34.97: 340 34.97 - 52.45: 60 52.45 - 69.94: 14 69.94 - 87.42: 8 Dihedral angle restraints: 4070 sinusoidal: 1733 harmonic: 2337 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 38.29 54.71 1 1.00e+01 1.00e-02 4.05e+01 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 55.17 37.83 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" CA CYS A 391 " pdb=" C CYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta harmonic sigma weight residual -180.00 -163.69 -16.31 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 4067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 588 0.046 - 0.093: 273 0.093 - 0.139: 86 0.139 - 0.185: 24 0.185 - 0.231: 5 Chirality restraints: 976 Sorted by residual: chirality pdb=" CA ASN A 360 " pdb=" N ASN A 360 " pdb=" C ASN A 360 " pdb=" CB ASN A 360 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 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 -2.37 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB THR A 333 " pdb=" CA THR A 333 " pdb=" OG1 THR A 333 " pdb=" CG2 THR A 333 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 973 not shown) Planarity restraints: 1186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS D 241 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.90e+00 pdb=" C HIS D 241 " 0.054 2.00e-02 2.50e+03 pdb=" O HIS D 241 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA D 242 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 244 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.52e+00 pdb=" C VAL D 244 " 0.050 2.00e-02 2.50e+03 pdb=" O VAL D 244 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG D 245 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 226 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.45e+00 pdb=" C VAL D 226 " 0.050 2.00e-02 2.50e+03 pdb=" O VAL D 226 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU D 227 " -0.017 2.00e-02 2.50e+03 ... (remaining 1183 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1832 2.81 - 3.33: 5953 3.33 - 3.85: 11478 3.85 - 4.38: 13089 4.38 - 4.90: 22516 Nonbonded interactions: 54868 Sorted by model distance: nonbonded pdb=" OH TYR D 183 " pdb=" OD1 ASP D 509 " model vdw 2.282 2.440 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.342 2.440 nonbonded pdb=" OE2 GLU D 435 " pdb=" NZ LYS D 541 " model vdw 2.343 2.520 nonbonded pdb=" OE1 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.350 2.440 nonbonded pdb=" OD1 ASP D 382 " pdb=" OH TYR D 385 " model vdw 2.360 2.440 ... (remaining 54863 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: 3.850 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: 14.860 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 20.250 Find NCS groups from input model: 0.150 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:13.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 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 0.072 6745 Z= 0.392 Angle : 0.937 12.179 9166 Z= 0.510 Chirality : 0.059 0.231 976 Planarity : 0.007 0.063 1179 Dihedral : 14.081 87.420 2552 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.57 % Allowed : 4.29 % Favored : 95.14 % 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: -0.08 (0.27), residues: 792 helix: 0.27 (0.23), residues: 389 sheet: 2.01 (0.81), residues: 34 loop : -0.50 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 594 HIS 0.007 0.002 HIS A 505 PHE 0.024 0.003 PHE A 377 TYR 0.031 0.002 TYR D 385 ARG 0.012 0.001 ARG A 457 *********************** 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 194 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 190 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ARG cc_start: 0.8165 (ptm160) cc_final: 0.7820 (ttt90) REVERT: A 465 GLU cc_start: 0.8263 (tt0) cc_final: 0.8028 (tt0) REVERT: D 55 THR cc_start: 0.8054 (m) cc_final: 0.7796 (p) REVERT: D 270 MET cc_start: 0.8145 (tpt) cc_final: 0.7927 (tpp) REVERT: D 366 MET cc_start: 0.8582 (ttp) cc_final: 0.8362 (ttp) REVERT: D 483 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8173 (tm-30) REVERT: D 534 LYS cc_start: 0.8626 (mmmt) cc_final: 0.8302 (mmtm) REVERT: D 582 ARG cc_start: 0.8046 (mmm160) cc_final: 0.7744 (mmm160) REVERT: D 603 PHE cc_start: 0.8656 (t80) cc_final: 0.8027 (t80) REVERT: D 604 VAL cc_start: 0.9243 (p) cc_final: 0.8911 (t) outliers start: 4 outliers final: 1 residues processed: 192 average time/residue: 1.3088 time to fit residues: 262.6440 Evaluate side-chains 118 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 609 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 0.0870 chunk 20 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 0.0370 chunk 71 optimal weight: 0.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN D 76 GLN ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN D 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6745 Z= 0.202 Angle : 0.581 7.302 9166 Z= 0.299 Chirality : 0.043 0.258 976 Planarity : 0.004 0.037 1179 Dihedral : 5.832 54.066 1014 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.58 % Allowed : 14.74 % Favored : 82.69 % 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: 0.87 (0.29), residues: 792 helix: 1.15 (0.25), residues: 402 sheet: 1.06 (0.75), residues: 43 loop : -0.06 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 165 HIS 0.004 0.001 HIS D 241 PHE 0.013 0.001 PHE D 369 TYR 0.014 0.001 TYR D 41 ARG 0.004 0.000 ARG D 582 *********************** 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 132 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 ASP cc_start: 0.7926 (p0) cc_final: 0.7556 (p0) REVERT: A 357 ARG cc_start: 0.8215 (ptm160) cc_final: 0.7807 (ttt90) REVERT: D 26 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8338 (mtmm) REVERT: D 55 THR cc_start: 0.8106 (m) cc_final: 0.7769 (p) REVERT: D 228 HIS cc_start: 0.8093 (t70) cc_final: 0.7864 (m90) REVERT: D 408 MET cc_start: 0.9230 (mmt) cc_final: 0.9027 (mmt) REVERT: D 429 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7980 (mm-40) REVERT: D 483 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7968 (tm-30) REVERT: D 497 TYR cc_start: 0.8758 (m-80) cc_final: 0.8482 (m-80) REVERT: D 603 PHE cc_start: 0.8667 (t80) cc_final: 0.8361 (t80) outliers start: 18 outliers final: 7 residues processed: 123 average time/residue: 1.4322 time to fit residues: 184.3138 Evaluate side-chains 112 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 429 GLN 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: 2.9990 chunk 59 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6745 Z= 0.268 Angle : 0.584 6.343 9166 Z= 0.296 Chirality : 0.043 0.189 976 Planarity : 0.004 0.032 1179 Dihedral : 5.119 43.460 1012 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.58 % Allowed : 15.31 % Favored : 81.12 % 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: 1.15 (0.29), residues: 792 helix: 1.29 (0.25), residues: 408 sheet: 0.92 (0.78), residues: 43 loop : 0.22 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 165 HIS 0.003 0.001 HIS D 535 PHE 0.018 0.001 PHE D 400 TYR 0.015 0.001 TYR D 50 ARG 0.003 0.000 ARG D 306 *********************** 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 131 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7976 (mp0) REVERT: D 26 LYS cc_start: 0.8638 (mtpt) cc_final: 0.8318 (mtmm) REVERT: D 182 GLU cc_start: 0.8340 (tt0) cc_final: 0.7999 (tt0) REVERT: D 243 TYR cc_start: 0.8948 (t80) cc_final: 0.8736 (t80) REVERT: D 287 GLN cc_start: 0.8482 (mp10) cc_final: 0.8275 (pm20) REVERT: D 467 GLU cc_start: 0.8208 (mp0) cc_final: 0.7415 (mp0) REVERT: D 483 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8047 (tm-30) REVERT: D 603 PHE cc_start: 0.8691 (t80) cc_final: 0.8355 (t80) outliers start: 25 outliers final: 12 residues processed: 120 average time/residue: 1.2287 time to fit residues: 154.8787 Evaluate side-chains 112 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 429 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 72 optimal weight: 0.3980 chunk 76 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 405 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6745 Z= 0.217 Angle : 0.555 7.128 9166 Z= 0.278 Chirality : 0.042 0.179 976 Planarity : 0.004 0.031 1179 Dihedral : 4.452 30.950 1012 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.01 % Allowed : 16.74 % Favored : 79.26 % 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: 1.35 (0.30), residues: 792 helix: 1.46 (0.25), residues: 408 sheet: 0.84 (0.78), residues: 43 loop : 0.35 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 165 HIS 0.003 0.001 HIS D 239 PHE 0.013 0.001 PHE D 369 TYR 0.013 0.001 TYR D 50 ARG 0.003 0.000 ARG A 493 *********************** 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 132 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 104 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 ASP cc_start: 0.7855 (p0) cc_final: 0.7638 (p0) REVERT: A 340 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: A 346 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7041 (ppp-140) REVERT: A 403 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8023 (ptp90) REVERT: D 26 LYS cc_start: 0.8627 (mtpt) cc_final: 0.8256 (mttp) REVERT: D 182 GLU cc_start: 0.8388 (tt0) cc_final: 0.8100 (tt0) REVERT: D 243 TYR cc_start: 0.8960 (t80) cc_final: 0.8758 (t80) REVERT: D 287 GLN cc_start: 0.8430 (mp10) cc_final: 0.8143 (pm20) REVERT: D 467 GLU cc_start: 0.8230 (mp0) cc_final: 0.7247 (mp0) REVERT: D 472 GLN cc_start: 0.8286 (mm-40) cc_final: 0.8052 (mm-40) REVERT: D 479 GLU cc_start: 0.8671 (tt0) cc_final: 0.8417 (mt-10) REVERT: D 483 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8012 (tm-30) REVERT: D 531 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.8038 (mt0) REVERT: D 596 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8891 (mtmm) REVERT: D 603 PHE cc_start: 0.8677 (t80) cc_final: 0.8363 (t80) outliers start: 28 outliers final: 15 residues processed: 120 average time/residue: 1.2697 time to fit residues: 159.9121 Evaluate side-chains 116 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 429 GLN Chi-restraints excluded: chain D residue 531 GLN 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: 0.3980 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.0970 chunk 44 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6745 Z= 0.208 Angle : 0.557 7.294 9166 Z= 0.280 Chirality : 0.041 0.163 976 Planarity : 0.003 0.030 1179 Dihedral : 4.241 29.238 1012 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.15 % Allowed : 16.88 % Favored : 78.97 % 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: 1.55 (0.30), residues: 792 helix: 1.64 (0.26), residues: 403 sheet: 1.77 (0.91), residues: 34 loop : 0.35 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 165 HIS 0.003 0.001 HIS D 239 PHE 0.013 0.001 PHE D 369 TYR 0.012 0.001 TYR D 50 ARG 0.004 0.000 ARG A 493 *********************** 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 134 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 105 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 ASP cc_start: 0.7852 (p0) cc_final: 0.7642 (p0) REVERT: A 340 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: A 346 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.7067 (ppp-140) REVERT: D 26 LYS cc_start: 0.8645 (mtpt) cc_final: 0.8266 (mttp) REVERT: D 115 ARG cc_start: 0.8753 (tpm170) cc_final: 0.8529 (tpm170) REVERT: D 182 GLU cc_start: 0.8396 (tt0) cc_final: 0.8102 (tt0) REVERT: D 213 ASP cc_start: 0.8554 (t70) cc_final: 0.8213 (t0) REVERT: D 287 GLN cc_start: 0.8441 (mp10) cc_final: 0.8168 (pm20) REVERT: D 305 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8290 (tm-30) REVERT: D 467 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: D 472 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7982 (mm-40) REVERT: D 479 GLU cc_start: 0.8664 (tt0) cc_final: 0.8366 (mt-10) REVERT: D 483 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8003 (tm-30) REVERT: D 497 TYR cc_start: 0.8633 (m-80) cc_final: 0.8252 (m-80) REVERT: D 531 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.8028 (mt0) REVERT: D 596 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8885 (mtmm) REVERT: D 603 PHE cc_start: 0.8677 (t80) cc_final: 0.8399 (t80) outliers start: 29 outliers final: 15 residues processed: 121 average time/residue: 1.2453 time to fit residues: 158.0458 Evaluate side-chains 120 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 429 GLN Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 596 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.8251 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6745 Z= 0.281 Angle : 0.585 7.715 9166 Z= 0.293 Chirality : 0.043 0.162 976 Planarity : 0.004 0.030 1179 Dihedral : 4.363 28.362 1012 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.29 % Allowed : 17.88 % Favored : 77.83 % 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: 1.54 (0.30), residues: 792 helix: 1.65 (0.26), residues: 403 sheet: 0.63 (0.81), residues: 44 loop : 0.45 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 478 HIS 0.003 0.001 HIS D 239 PHE 0.015 0.001 PHE D 400 TYR 0.013 0.001 TYR D 385 ARG 0.004 0.000 ARG A 493 *********************** 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 133 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 103 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 26 LYS cc_start: 0.8627 (mtpt) cc_final: 0.8274 (mttm) REVERT: D 182 GLU cc_start: 0.8470 (tt0) cc_final: 0.8178 (tt0) REVERT: D 213 ASP cc_start: 0.8575 (t70) cc_final: 0.8248 (t0) REVERT: D 287 GLN cc_start: 0.8442 (mp10) cc_final: 0.8171 (pm20) REVERT: D 305 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8281 (tm-30) REVERT: D 467 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: D 479 GLU cc_start: 0.8633 (tt0) cc_final: 0.8337 (mt-10) REVERT: D 483 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8043 (tm-30) REVERT: D 497 TYR cc_start: 0.8686 (m-80) cc_final: 0.8281 (m-80) REVERT: D 531 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7999 (mt0) REVERT: D 596 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8882 (mtmm) REVERT: D 603 PHE cc_start: 0.8652 (t80) cc_final: 0.8329 (t80) outliers start: 30 outliers final: 17 residues processed: 120 average time/residue: 1.2719 time to fit residues: 160.2709 Evaluate side-chains 115 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 429 GLN Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 596 LYS 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: 1.9990 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 0.1980 chunk 47 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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: 0.8233 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 0.035 6745 Z= 0.215 Angle : 0.573 8.340 9166 Z= 0.286 Chirality : 0.042 0.153 976 Planarity : 0.003 0.030 1179 Dihedral : 4.230 27.752 1012 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.58 % Allowed : 18.45 % Favored : 77.97 % 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: 1.51 (0.30), residues: 792 helix: 1.68 (0.26), residues: 403 sheet: 1.64 (0.92), residues: 34 loop : 0.24 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 165 HIS 0.003 0.001 HIS D 374 PHE 0.013 0.001 PHE D 369 TYR 0.011 0.001 TYR D 50 ARG 0.004 0.000 ARG A 493 *********************** 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 123 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 98 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 26 LYS cc_start: 0.8649 (mtpt) cc_final: 0.8290 (mttm) REVERT: D 182 GLU cc_start: 0.8481 (tt0) cc_final: 0.8161 (tt0) REVERT: D 213 ASP cc_start: 0.8554 (t70) cc_final: 0.8238 (t0) REVERT: D 287 GLN cc_start: 0.8432 (mp10) cc_final: 0.8160 (pm20) REVERT: D 305 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8287 (tm-30) REVERT: D 467 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: D 472 GLN cc_start: 0.8166 (mm110) cc_final: 0.7958 (mm-40) REVERT: D 479 GLU cc_start: 0.8627 (tt0) cc_final: 0.8322 (mt-10) REVERT: D 483 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8064 (tm-30) REVERT: D 497 TYR cc_start: 0.8731 (m-80) cc_final: 0.8309 (m-80) REVERT: D 531 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.8035 (mt0) REVERT: D 596 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8878 (mtmm) REVERT: D 603 PHE cc_start: 0.8643 (t80) cc_final: 0.8329 (t80) outliers start: 25 outliers final: 14 residues processed: 114 average time/residue: 1.2885 time to fit residues: 154.2008 Evaluate side-chains 116 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 429 GLN Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 596 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 51 optimal weight: 0.1980 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 59 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8229 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6745 Z= 0.207 Angle : 0.566 8.755 9166 Z= 0.281 Chirality : 0.042 0.152 976 Planarity : 0.003 0.029 1179 Dihedral : 4.149 28.088 1012 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.43 % Allowed : 19.17 % Favored : 77.40 % 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: 1.52 (0.30), residues: 792 helix: 1.78 (0.26), residues: 396 sheet: 1.50 (0.90), residues: 34 loop : 0.18 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 165 HIS 0.003 0.001 HIS D 374 PHE 0.013 0.001 PHE D 369 TYR 0.011 0.001 TYR D 41 ARG 0.003 0.000 ARG A 493 *********************** 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 121 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8215 (mp0) cc_final: 0.8011 (mp0) REVERT: D 26 LYS cc_start: 0.8647 (mtpt) cc_final: 0.8267 (mttp) REVERT: D 182 GLU cc_start: 0.8471 (tt0) cc_final: 0.8139 (tt0) REVERT: D 213 ASP cc_start: 0.8546 (t70) cc_final: 0.8240 (t0) REVERT: D 238 GLU cc_start: 0.8607 (tt0) cc_final: 0.8292 (tt0) REVERT: D 243 TYR cc_start: 0.8915 (t80) cc_final: 0.8682 (t80) REVERT: D 287 GLN cc_start: 0.8440 (mp10) cc_final: 0.8171 (pm20) REVERT: D 305 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8273 (tm-30) REVERT: D 467 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: D 472 GLN cc_start: 0.8226 (mm110) cc_final: 0.7988 (mm-40) REVERT: D 479 GLU cc_start: 0.8625 (tt0) cc_final: 0.8306 (mt-10) REVERT: D 483 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8057 (tm-30) REVERT: D 497 TYR cc_start: 0.8784 (m-80) cc_final: 0.8377 (m-80) REVERT: D 596 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8842 (mtmm) REVERT: D 603 PHE cc_start: 0.8652 (t80) cc_final: 0.8347 (t80) outliers start: 24 outliers final: 13 residues processed: 112 average time/residue: 1.2638 time to fit residues: 148.4691 Evaluate side-chains 112 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 429 GLN Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain D residue 596 LYS 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: 2.9990 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 0.0570 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- 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: 0.8237 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6745 Z= 0.235 Angle : 0.583 9.047 9166 Z= 0.290 Chirality : 0.042 0.153 976 Planarity : 0.003 0.029 1179 Dihedral : 4.195 27.851 1012 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.72 % Allowed : 20.03 % Favored : 77.25 % 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: 1.49 (0.30), residues: 792 helix: 1.75 (0.26), residues: 396 sheet: 1.02 (0.86), residues: 39 loop : 0.22 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 41 ARG 0.004 0.000 ARG A 493 *********************** 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 115 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 26 LYS cc_start: 0.8650 (mtpt) cc_final: 0.8270 (mttp) REVERT: D 182 GLU cc_start: 0.8501 (tt0) cc_final: 0.8171 (tt0) REVERT: D 213 ASP cc_start: 0.8545 (t70) cc_final: 0.8248 (t0) REVERT: D 238 GLU cc_start: 0.8611 (tt0) cc_final: 0.8294 (tt0) REVERT: D 287 GLN cc_start: 0.8429 (mp10) cc_final: 0.8160 (pm20) REVERT: D 305 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8225 (tm-30) REVERT: D 467 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: D 479 GLU cc_start: 0.8642 (tt0) cc_final: 0.8263 (mt-10) REVERT: D 483 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8017 (tm-30) REVERT: D 497 TYR cc_start: 0.8800 (m-80) cc_final: 0.8400 (m-80) REVERT: D 596 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8847 (mtmm) REVERT: D 603 PHE cc_start: 0.8649 (t80) cc_final: 0.8382 (t80) outliers start: 19 outliers final: 12 residues processed: 107 average time/residue: 1.2314 time to fit residues: 138.5487 Evaluate side-chains 109 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 429 GLN Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain D residue 596 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 62 optimal weight: 0.0980 chunk 6 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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: 0.8218 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6745 Z= 0.190 Angle : 0.577 9.379 9166 Z= 0.285 Chirality : 0.041 0.154 976 Planarity : 0.003 0.029 1179 Dihedral : 4.079 28.507 1012 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.72 % Allowed : 20.89 % Favored : 77.40 % 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: 1.46 (0.30), residues: 792 helix: 1.71 (0.26), residues: 404 sheet: 0.99 (0.87), residues: 39 loop : 0.18 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 165 HIS 0.003 0.001 HIS D 374 PHE 0.013 0.001 PHE D 369 TYR 0.010 0.001 TYR D 41 ARG 0.003 0.000 ARG A 493 ********************** 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 110 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 26 LYS cc_start: 0.8642 (mtpt) cc_final: 0.8247 (mttp) REVERT: D 182 GLU cc_start: 0.8453 (tt0) cc_final: 0.8112 (tt0) REVERT: D 213 ASP cc_start: 0.8534 (t70) cc_final: 0.8237 (t0) REVERT: D 287 GLN cc_start: 0.8396 (mp10) cc_final: 0.8145 (pm20) REVERT: D 305 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8236 (tm-30) REVERT: D 467 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: D 479 GLU cc_start: 0.8618 (tt0) cc_final: 0.8287 (mt-10) REVERT: D 483 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8071 (tm-30) REVERT: D 497 TYR cc_start: 0.8828 (m-80) cc_final: 0.8462 (m-80) REVERT: D 582 ARG cc_start: 0.7950 (mmm-85) cc_final: 0.7711 (mmm160) REVERT: D 596 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8850 (mtmm) REVERT: D 603 PHE cc_start: 0.8646 (t80) cc_final: 0.8382 (t80) outliers start: 12 outliers final: 9 residues processed: 107 average time/residue: 1.2492 time to fit residues: 140.7215 Evaluate side-chains 107 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain D residue 596 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.3400 r_free = 0.3400 target = 0.098621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.075780 restraints weight = 12115.265| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.80 r_work: 0.2893 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6745 Z= 0.273 Angle : 0.609 9.292 9166 Z= 0.303 Chirality : 0.043 0.153 976 Planarity : 0.003 0.029 1179 Dihedral : 4.301 28.055 1012 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.15 % Allowed : 20.74 % Favored : 77.11 % 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: 1.45 (0.30), residues: 792 helix: 1.64 (0.26), residues: 403 sheet: 0.30 (0.73), residues: 49 loop : 0.36 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 478 HIS 0.003 0.001 HIS D 239 PHE 0.014 0.001 PHE D 369 TYR 0.012 0.001 TYR D 385 ARG 0.004 0.000 ARG A 493 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3218.13 seconds wall clock time: 57 minutes 41.94 seconds (3461.94 seconds total)