Starting phenix.real_space_refine on Sat Apr 6 00:15:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrl_37779/04_2024/8wrl_37779.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrl_37779/04_2024/8wrl_37779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrl_37779/04_2024/8wrl_37779.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrl_37779/04_2024/8wrl_37779.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrl_37779/04_2024/8wrl_37779.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrl_37779/04_2024/8wrl_37779.pdb" } resolution = 3.36 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= 0.083 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 4143 2.51 5 N 1070 2.21 5 O 1222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A ASP 201": "OD1" <-> "OD2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 299": "OD1" <-> "OD2" Residue "A GLU 312": "OE1" <-> "OE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A ASP 499": "OD1" <-> "OD2" Residue "A TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6472 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 27, 'TRANS': 566} Chain: "B" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1557 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 13, 'TRANS': 182} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" 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 Time building chain proxies: 3.82, per 1000 atoms: 0.59 Number of scatterers: 6472 At special positions: 0 Unit cell: (74.336, 89.688, 117.968, 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 1222 8.00 N 1070 7.00 C 4143 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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 A 701 " - " ASN A 546 " " NAG A 702 " - " ASN A 90 " " NAG A 703 " - " ASN A 322 " " NAG A 704 " - " ASN A 53 " " NAG B 601 " - " ASN B 343 " Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.3 seconds 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 7 sheets defined 52.3% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 20 through 52 removed outlier: 3.514A pdb=" N LYS A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.090A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 157 through 193 removed outlier: 4.289A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.564A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 218 through 252 Proline residue: A 235 - end of helix removed outlier: 4.002A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 281 removed outlier: 3.718A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.765A pdb=" N GLN A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.529A pdb=" N GLY A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 365 through 375 Processing helix chain 'A' and resid 376 through 385 removed outlier: 3.566A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 398 through 413 removed outlier: 4.600A pdb=" N GLU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 444 Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 473 through 484 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 531 removed outlier: 3.821A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.601A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 542' Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.025A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.917A pdb=" N GLU A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.723A pdb=" N PHE B 371 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.594A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.042A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.809A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.446A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'B' and resid 473 through 474 301 hydrogen bonds defined for protein. 843 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: 1.57 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1177 1.33 - 1.45: 1839 1.45 - 1.57: 3582 1.57 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 6656 Sorted by residual: bond pdb=" CG HIS A 378 " pdb=" CD2 HIS A 378 " ideal model delta sigma weight residual 1.354 1.318 0.036 1.10e-02 8.26e+03 1.05e+01 bond pdb=" N THR A 371 " pdb=" CA THR A 371 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.33e-02 5.65e+03 7.00e+00 bond pdb=" CA ALA A 372 " pdb=" CB ALA A 372 " ideal model delta sigma weight residual 1.530 1.486 0.044 1.68e-02 3.54e+03 6.84e+00 bond pdb=" CG HIS A 373 " pdb=" CD2 HIS A 373 " ideal model delta sigma weight residual 1.354 1.326 0.028 1.10e-02 8.26e+03 6.49e+00 bond pdb=" N GLU A 375 " pdb=" CA GLU A 375 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.22e-02 6.72e+03 6.41e+00 ... (remaining 6651 not shown) Histogram of bond angle deviations from ideal: 97.49 - 104.80: 120 104.80 - 112.11: 3155 112.11 - 119.42: 2288 119.42 - 126.73: 3343 126.73 - 134.03: 140 Bond angle restraints: 9046 Sorted by residual: angle pdb=" N MET A 376 " pdb=" CA MET A 376 " pdb=" C MET A 376 " ideal model delta sigma weight residual 114.31 101.82 12.49 1.29e+00 6.01e-01 9.37e+01 angle pdb=" C HIS A 378 " pdb=" N ILE A 379 " pdb=" CA ILE A 379 " ideal model delta sigma weight residual 121.02 108.14 12.88 1.51e+00 4.39e-01 7.28e+01 angle pdb=" CA HIS A 373 " pdb=" CB HIS A 373 " pdb=" CG HIS A 373 " ideal model delta sigma weight residual 113.80 121.23 -7.43 1.00e+00 1.00e+00 5.52e+01 angle pdb=" N GLU A 375 " pdb=" CA GLU A 375 " pdb=" C GLU A 375 " ideal model delta sigma weight residual 112.88 104.91 7.97 1.29e+00 6.01e-01 3.82e+01 angle pdb=" CA HIS A 378 " pdb=" CB HIS A 378 " pdb=" CG HIS A 378 " ideal model delta sigma weight residual 113.80 118.66 -4.86 1.00e+00 1.00e+00 2.36e+01 ... (remaining 9041 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.10: 3448 21.10 - 42.19: 432 42.19 - 63.29: 82 63.29 - 84.39: 17 84.39 - 105.49: 18 Dihedral angle restraints: 3997 sinusoidal: 1677 harmonic: 2320 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual 93.00 22.41 70.59 1 1.00e+01 1.00e-02 6.41e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -45.95 -40.05 1 1.00e+01 1.00e-02 2.25e+01 dihedral pdb=" CA TRP A 349 " pdb=" C TRP A 349 " pdb=" N ASP A 350 " pdb=" CA ASP A 350 " ideal model delta harmonic sigma weight residual 180.00 157.51 22.49 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 3994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 724 0.046 - 0.091: 171 0.091 - 0.137: 56 0.137 - 0.182: 6 0.182 - 0.227: 2 Chirality restraints: 959 Sorted by residual: chirality pdb=" CA GLU A 375 " pdb=" N GLU A 375 " pdb=" C GLU A 375 " pdb=" CB GLU A 375 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB THR A 122 " pdb=" CA THR A 122 " pdb=" OG1 THR A 122 " pdb=" CG2 THR A 122 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA MET A 376 " pdb=" N MET A 376 " pdb=" C MET A 376 " pdb=" CB MET A 376 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.22e-01 ... (remaining 956 not shown) Planarity restraints: 1171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 370 " -0.019 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C LEU A 370 " 0.061 2.00e-02 2.50e+03 pdb=" O LEU A 370 " -0.022 2.00e-02 2.50e+03 pdb=" N THR A 371 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 478 " 0.052 5.00e-02 4.00e+02 7.62e-02 9.30e+00 pdb=" N PRO B 479 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 479 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 479 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 378 " 0.012 2.00e-02 2.50e+03 2.54e-02 6.46e+00 pdb=" C HIS A 378 " -0.044 2.00e-02 2.50e+03 pdb=" O HIS A 378 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE A 379 " 0.015 2.00e-02 2.50e+03 ... (remaining 1168 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 22 2.40 - 3.02: 3617 3.02 - 3.65: 9842 3.65 - 4.27: 14297 4.27 - 4.90: 24817 Nonbonded interactions: 52595 Sorted by model distance: nonbonded pdb=" OH TYR A 279 " pdb=" O LYS A 441 " model vdw 1.771 2.440 nonbonded pdb=" CB PRO A 346 " pdb=" SD MET A 360 " model vdw 1.931 3.800 nonbonded pdb=" O ALA A 372 " pdb=" CG MET A 376 " model vdw 2.076 3.440 nonbonded pdb=" CD1 ILE A 358 " pdb=" SD MET A 376 " model vdw 2.152 3.820 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.229 2.440 ... (remaining 52590 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: 1.050 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: 3.780 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 20.590 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 6656 Z= 0.275 Angle : 0.699 12.884 9046 Z= 0.410 Chirality : 0.045 0.227 959 Planarity : 0.005 0.076 1166 Dihedral : 19.509 105.486 2489 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.58 % Allowed : 23.34 % Favored : 76.08 % 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: -0.27 (0.30), residues: 786 helix: 0.69 (0.27), residues: 365 sheet: -0.64 (0.76), residues: 35 loop : -0.96 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 594 HIS 0.013 0.001 HIS A 373 PHE 0.009 0.001 PHE A 32 TYR 0.030 0.002 TYR A 243 ARG 0.003 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.695 Fit side-chains REVERT: A 442 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7571 (mm-40) REVERT: A 483 GLU cc_start: 0.7827 (mp0) cc_final: 0.7485 (mp0) outliers start: 4 outliers final: 3 residues processed: 84 average time/residue: 0.1550 time to fit residues: 18.3325 Evaluate side-chains 77 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 468 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.0780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6656 Z= 0.207 Angle : 0.522 8.117 9046 Z= 0.261 Chirality : 0.042 0.195 959 Planarity : 0.004 0.038 1166 Dihedral : 8.895 60.698 965 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.31 % Allowed : 22.19 % Favored : 74.50 % 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: 0.08 (0.31), residues: 786 helix: 0.99 (0.28), residues: 376 sheet: -0.51 (0.81), residues: 35 loop : -0.84 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 566 HIS 0.005 0.001 HIS A 378 PHE 0.011 0.001 PHE A 32 TYR 0.013 0.001 TYR B 453 ARG 0.002 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 0.786 Fit side-chains REVERT: A 87 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7132 (tm-30) REVERT: A 299 ASP cc_start: 0.6898 (m-30) cc_final: 0.6555 (m-30) REVERT: A 483 GLU cc_start: 0.7908 (mp0) cc_final: 0.7519 (mp0) outliers start: 23 outliers final: 11 residues processed: 95 average time/residue: 0.1731 time to fit residues: 22.8062 Evaluate side-chains 88 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 chunk 63 optimal weight: 0.0070 chunk 24 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6656 Z= 0.156 Angle : 0.485 6.238 9046 Z= 0.241 Chirality : 0.040 0.232 959 Planarity : 0.003 0.030 1166 Dihedral : 5.700 59.583 963 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.16 % Allowed : 23.78 % Favored : 74.06 % 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: 0.16 (0.31), residues: 786 helix: 1.11 (0.28), residues: 384 sheet: -0.50 (0.71), residues: 45 loop : -0.89 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.004 0.001 HIS A 34 PHE 0.008 0.001 PHE A 523 TYR 0.010 0.001 TYR A 385 ARG 0.001 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.781 Fit side-chains REVERT: A 87 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7136 (tm-30) REVERT: A 299 ASP cc_start: 0.6982 (m-30) cc_final: 0.6686 (m-30) REVERT: A 483 GLU cc_start: 0.7960 (mp0) cc_final: 0.7750 (mm-30) REVERT: A 544 ILE cc_start: 0.5780 (OUTLIER) cc_final: 0.5434 (mt) outliers start: 15 outliers final: 11 residues processed: 93 average time/residue: 0.1634 time to fit residues: 21.1809 Evaluate side-chains 90 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6656 Z= 0.192 Angle : 0.495 5.469 9046 Z= 0.249 Chirality : 0.040 0.189 959 Planarity : 0.003 0.028 1166 Dihedral : 5.340 59.112 963 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.89 % Allowed : 23.05 % Favored : 73.05 % 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: 0.21 (0.31), residues: 786 helix: 1.17 (0.28), residues: 384 sheet: -0.57 (0.70), residues: 45 loop : -0.90 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 566 HIS 0.003 0.001 HIS A 34 PHE 0.011 0.001 PHE A 523 TYR 0.012 0.001 TYR B 453 ARG 0.001 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 87 time to evaluate : 0.678 Fit side-chains REVERT: A 87 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7116 (tm-30) REVERT: A 299 ASP cc_start: 0.6990 (m-30) cc_final: 0.6720 (m-30) REVERT: A 544 ILE cc_start: 0.5876 (OUTLIER) cc_final: 0.5570 (mt) outliers start: 27 outliers final: 18 residues processed: 104 average time/residue: 0.1598 time to fit residues: 23.6030 Evaluate side-chains 100 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.0870 chunk 64 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6656 Z= 0.165 Angle : 0.483 5.954 9046 Z= 0.243 Chirality : 0.040 0.206 959 Planarity : 0.003 0.028 1166 Dihedral : 4.972 56.120 963 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.89 % Allowed : 22.77 % Favored : 73.34 % 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: 0.28 (0.31), residues: 786 helix: 1.25 (0.28), residues: 384 sheet: -0.50 (0.70), residues: 45 loop : -0.88 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 275 HIS 0.004 0.001 HIS A 34 PHE 0.008 0.001 PHE A 523 TYR 0.010 0.001 TYR B 453 ARG 0.001 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 86 time to evaluate : 0.681 Fit side-chains REVERT: A 87 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7232 (tm-30) REVERT: A 150 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7212 (tm-30) REVERT: A 299 ASP cc_start: 0.7014 (m-30) cc_final: 0.6755 (m-30) REVERT: A 398 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7800 (pm20) REVERT: A 535 HIS cc_start: 0.7279 (t-90) cc_final: 0.7053 (t-90) REVERT: A 544 ILE cc_start: 0.5847 (OUTLIER) cc_final: 0.5523 (mt) outliers start: 27 outliers final: 20 residues processed: 105 average time/residue: 0.1558 time to fit residues: 23.5213 Evaluate side-chains 105 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 82 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6656 Z= 0.213 Angle : 0.502 5.963 9046 Z= 0.255 Chirality : 0.041 0.215 959 Planarity : 0.003 0.027 1166 Dihedral : 4.921 54.436 963 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.18 % Allowed : 22.05 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.31), residues: 786 helix: 1.23 (0.28), residues: 384 sheet: -0.62 (0.70), residues: 45 loop : -0.87 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 271 HIS 0.004 0.001 HIS A 34 PHE 0.008 0.001 PHE A 523 TYR 0.013 0.001 TYR B 453 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 86 time to evaluate : 0.731 Fit side-chains REVERT: A 87 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7193 (tm-30) REVERT: A 150 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7206 (tm-30) REVERT: A 299 ASP cc_start: 0.7026 (m-30) cc_final: 0.6774 (m-30) REVERT: A 467 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6870 (mt-10) REVERT: A 535 HIS cc_start: 0.7327 (t-90) cc_final: 0.7108 (t-90) REVERT: A 544 ILE cc_start: 0.5892 (OUTLIER) cc_final: 0.5565 (mt) outliers start: 29 outliers final: 23 residues processed: 108 average time/residue: 0.1586 time to fit residues: 24.4443 Evaluate side-chains 108 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 82 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 0.0060 chunk 75 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 45 optimal weight: 0.1980 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6656 Z= 0.149 Angle : 0.479 5.358 9046 Z= 0.242 Chirality : 0.040 0.211 959 Planarity : 0.003 0.028 1166 Dihedral : 4.661 52.841 963 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.75 % Allowed : 22.33 % Favored : 73.92 % 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: 0.39 (0.31), residues: 786 helix: 1.35 (0.28), residues: 383 sheet: -0.37 (0.71), residues: 45 loop : -0.84 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 271 HIS 0.003 0.001 HIS A 493 PHE 0.009 0.001 PHE B 374 TYR 0.010 0.001 TYR A 516 ARG 0.001 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 88 time to evaluate : 1.126 Fit side-chains REVERT: A 87 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7239 (tm-30) REVERT: A 150 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7168 (tm-30) REVERT: A 398 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7742 (pm20) REVERT: B 378 LYS cc_start: 0.8141 (mmtt) cc_final: 0.7710 (mmtm) outliers start: 26 outliers final: 21 residues processed: 104 average time/residue: 0.1610 time to fit residues: 23.4806 Evaluate side-chains 109 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 86 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6656 Z= 0.186 Angle : 0.501 6.531 9046 Z= 0.254 Chirality : 0.041 0.223 959 Planarity : 0.003 0.027 1166 Dihedral : 4.678 50.995 963 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.18 % Allowed : 22.62 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.31), residues: 786 helix: 1.29 (0.28), residues: 387 sheet: -0.77 (0.77), residues: 40 loop : -0.80 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 271 HIS 0.003 0.001 HIS A 34 PHE 0.031 0.001 PHE B 374 TYR 0.012 0.001 TYR B 453 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 82 time to evaluate : 0.719 Fit side-chains REVERT: A 87 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7235 (tm-30) REVERT: A 150 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7199 (tm-30) REVERT: A 398 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7775 (pm20) REVERT: A 467 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6872 (mt-10) REVERT: A 483 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7799 (mm-30) REVERT: A 535 HIS cc_start: 0.7146 (t-90) cc_final: 0.6414 (t-90) REVERT: B 378 LYS cc_start: 0.8104 (mmtt) cc_final: 0.7665 (mmtm) outliers start: 29 outliers final: 22 residues processed: 102 average time/residue: 0.1687 time to fit residues: 24.1091 Evaluate side-chains 107 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 82 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 0.0370 chunk 35 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6656 Z= 0.170 Angle : 0.492 6.308 9046 Z= 0.250 Chirality : 0.040 0.221 959 Planarity : 0.003 0.028 1166 Dihedral : 4.593 50.453 963 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.89 % Allowed : 22.77 % Favored : 73.34 % 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: 0.40 (0.31), residues: 786 helix: 1.33 (0.28), residues: 387 sheet: -0.65 (0.77), residues: 40 loop : -0.79 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 271 HIS 0.003 0.001 HIS A 34 PHE 0.028 0.001 PHE B 374 TYR 0.011 0.001 TYR B 453 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 82 time to evaluate : 0.734 Fit side-chains REVERT: A 87 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7238 (tm-30) REVERT: A 150 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7205 (tm-30) REVERT: A 398 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7779 (pm20) REVERT: A 467 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6837 (mt-10) REVERT: A 483 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7780 (mm-30) REVERT: A 535 HIS cc_start: 0.7188 (t-90) cc_final: 0.6518 (t-90) REVERT: A 589 GLU cc_start: 0.8100 (tp30) cc_final: 0.7878 (tp30) REVERT: B 378 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7648 (mmtm) outliers start: 27 outliers final: 22 residues processed: 101 average time/residue: 0.1524 time to fit residues: 21.8436 Evaluate side-chains 106 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 81 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6656 Z= 0.201 Angle : 0.506 7.175 9046 Z= 0.258 Chirality : 0.041 0.229 959 Planarity : 0.003 0.027 1166 Dihedral : 4.679 50.481 963 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.89 % Allowed : 22.62 % Favored : 73.49 % 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: 0.35 (0.31), residues: 786 helix: 1.24 (0.27), residues: 388 sheet: -0.73 (0.76), residues: 40 loop : -0.75 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 271 HIS 0.004 0.001 HIS A 34 PHE 0.025 0.001 PHE B 374 TYR 0.012 0.001 TYR B 453 ARG 0.001 0.000 ARG A 460 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 83 time to evaluate : 0.670 Fit side-chains REVERT: A 87 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7223 (tm-30) REVERT: A 150 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7211 (tm-30) REVERT: A 398 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7811 (pm20) REVERT: A 467 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6877 (mt-10) REVERT: A 483 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7739 (mm-30) REVERT: A 535 HIS cc_start: 0.7203 (t-90) cc_final: 0.6538 (t-90) REVERT: A 589 GLU cc_start: 0.8099 (tp30) cc_final: 0.7885 (tp30) REVERT: B 378 LYS cc_start: 0.8119 (mmtt) cc_final: 0.7696 (mmtm) outliers start: 27 outliers final: 22 residues processed: 103 average time/residue: 0.1564 time to fit residues: 22.9265 Evaluate side-chains 107 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 82 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 0.0980 chunk 41 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.199113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.150675 restraints weight = 6718.306| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.93 r_work: 0.3316 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 6656 Z= 0.150 Angle : 0.482 5.943 9046 Z= 0.245 Chirality : 0.040 0.222 959 Planarity : 0.003 0.028 1166 Dihedral : 4.484 49.256 963 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.89 % Allowed : 22.77 % Favored : 73.34 % 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: 0.43 (0.31), residues: 786 helix: 1.32 (0.27), residues: 388 sheet: -0.61 (0.78), residues: 40 loop : -0.74 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 271 HIS 0.004 0.001 HIS A 34 PHE 0.018 0.001 PHE B 374 TYR 0.010 0.001 TYR A 516 ARG 0.001 0.000 ARG A 460 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1747.71 seconds wall clock time: 32 minutes 46.20 seconds (1966.20 seconds total)