Starting phenix.real_space_refine on Fri Dec 8 01:25:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrl_37779/12_2023/8wrl_37779.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrl_37779/12_2023/8wrl_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_37779/12_2023/8wrl_37779.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrl_37779/12_2023/8wrl_37779.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrl_37779/12_2023/8wrl_37779.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrl_37779/12_2023/8wrl_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-1.21rc1-5172/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: 3.66, per 1000 atoms: 0.57 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: 2.07 Conformation dependent library (CDL) restraints added in 1.2 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: 1.73 Time building geometry restraints manager: 2.30 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: 0.740 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: 3.860 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 19.950 Find NCS groups from input model: 0.170 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.680 ------------------------------------------------------------------------------- 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 : 0.739 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 84 average time/residue: 0.1656 time to fit residues: 19.6281 Evaluate side-chains 78 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.759 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0659 time to fit residues: 1.4661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 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: 0.9782 ------------------------------------------------------------------------------- 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: 0.0801 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= 0.205 Angle : 0.522 8.083 9046 Z= 0.261 Chirality : 0.042 0.188 959 Planarity : 0.004 0.038 1166 Dihedral : 8.778 59.927 961 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.17 % Allowed : 22.05 % Favored : 74.78 % 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: 0.08 (0.31), residues: 786 helix: 0.99 (0.28), residues: 376 sheet: -0.50 (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 473 HIS 0.005 0.001 HIS A 378 PHE 0.011 0.001 PHE A 32 TYR 0.013 0.001 TYR A 381 ARG 0.003 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 104 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 82 time to evaluate : 0.647 Fit side-chains outliers start: 22 outliers final: 9 residues processed: 96 average time/residue: 0.1614 time to fit residues: 21.4695 Evaluate side-chains 88 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.699 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0597 time to fit residues: 2.2165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 0.0870 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 70 optimal weight: 0.0870 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 24 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- 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: 0.7371 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6656 Z= 0.146 Angle : 0.483 6.358 9046 Z= 0.240 Chirality : 0.040 0.229 959 Planarity : 0.003 0.029 1166 Dihedral : 5.690 59.521 961 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.59 % Allowed : 23.63 % Favored : 74.78 % 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: 0.20 (0.31), residues: 786 helix: 1.15 (0.28), residues: 384 sheet: -0.27 (0.79), residues: 35 loop : -0.91 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.003 0.000 HIS A 34 PHE 0.007 0.001 PHE A 523 TYR 0.010 0.001 TYR A 516 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 95 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.702 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 89 average time/residue: 0.1670 time to fit residues: 20.9159 Evaluate side-chains 85 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.666 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0754 time to fit residues: 1.9394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 535 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.1138 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= 0.174 Angle : 0.484 5.414 9046 Z= 0.243 Chirality : 0.040 0.184 959 Planarity : 0.003 0.028 1166 Dihedral : 5.258 59.096 961 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.73 % Allowed : 23.49 % Favored : 74.78 % 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: 0.27 (0.31), residues: 786 helix: 1.22 (0.28), residues: 384 sheet: -0.49 (0.70), residues: 45 loop : -0.88 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 566 HIS 0.004 0.001 HIS A 34 PHE 0.009 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 93 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.689 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 88 average time/residue: 0.1536 time to fit residues: 19.2431 Evaluate side-chains 81 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.753 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0602 time to fit residues: 1.5227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0000 chunk 64 optimal weight: 0.0670 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 19 optimal weight: 0.0980 chunk 25 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.4124 ------------------------------------------------------------------------------- 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 A 535 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6656 Z= 0.136 Angle : 0.468 5.162 9046 Z= 0.234 Chirality : 0.039 0.200 959 Planarity : 0.003 0.028 1166 Dihedral : 4.802 55.197 961 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.44 % Allowed : 24.35 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.31), residues: 786 helix: 1.37 (0.28), residues: 384 sheet: -0.10 (0.80), residues: 35 loop : -0.82 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 165 HIS 0.003 0.000 HIS A 34 PHE 0.007 0.001 PHE A 523 TYR 0.010 0.001 TYR A 516 ARG 0.001 0.000 ARG B 454 *********************** 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 95 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.680 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 90 average time/residue: 0.1657 time to fit residues: 21.1185 Evaluate side-chains 84 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.694 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0725 time to fit residues: 1.3980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 0.0670 chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 535 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6656 Z= 0.253 Angle : 0.528 5.755 9046 Z= 0.267 Chirality : 0.042 0.220 959 Planarity : 0.003 0.027 1166 Dihedral : 4.929 53.808 961 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.30 % Allowed : 23.92 % Favored : 74.78 % 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: 0.28 (0.31), residues: 786 helix: 1.24 (0.28), residues: 383 sheet: -0.65 (0.68), residues: 45 loop : -0.85 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 271 HIS 0.004 0.001 HIS A 34 PHE 0.010 0.001 PHE A 32 TYR 0.015 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 95 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.640 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 91 average time/residue: 0.1627 time to fit residues: 21.0518 Evaluate side-chains 87 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.710 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0646 time to fit residues: 1.7932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 chunk 75 optimal weight: 0.6980 chunk 47 optimal weight: 0.3980 chunk 45 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 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 194 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6656 Z= 0.153 Angle : 0.486 5.447 9046 Z= 0.247 Chirality : 0.041 0.213 959 Planarity : 0.003 0.029 1166 Dihedral : 4.675 53.213 961 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.86 % Allowed : 24.78 % Favored : 74.35 % 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: 1.38 (0.28), residues: 381 sheet: -0.39 (0.71), residues: 45 loop : -0.80 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 271 HIS 0.003 0.001 HIS A 493 PHE 0.008 0.001 PHE B 429 TYR 0.011 0.001 TYR A 516 ARG 0.002 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 88 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.690 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 85 average time/residue: 0.1604 time to fit residues: 19.3751 Evaluate side-chains 83 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 0.696 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0618 time to fit residues: 1.2423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 51 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 68 optimal weight: 0.4980 chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 70 optimal weight: 0.0870 chunk 42 optimal weight: 2.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 6656 Z= 0.156 Angle : 0.492 6.746 9046 Z= 0.249 Chirality : 0.041 0.216 959 Planarity : 0.003 0.028 1166 Dihedral : 4.570 50.947 961 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.29 % Allowed : 25.50 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.31), residues: 786 helix: 1.41 (0.28), residues: 381 sheet: -0.61 (0.78), residues: 40 loop : -0.74 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 168 HIS 0.004 0.001 HIS A 493 PHE 0.030 0.001 PHE B 374 TYR 0.010 0.001 TYR A 516 ARG 0.001 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 81 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 0.740 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 80 average time/residue: 0.1810 time to fit residues: 20.3801 Evaluate side-chains 79 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.734 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 63 optimal weight: 0.4980 chunk 66 optimal weight: 0.1980 chunk 69 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 6656 Z= 0.150 Angle : 0.484 5.822 9046 Z= 0.244 Chirality : 0.040 0.217 959 Planarity : 0.003 0.028 1166 Dihedral : 4.407 48.685 961 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.72 % Allowed : 24.78 % 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: 0.50 (0.31), residues: 786 helix: 1.41 (0.27), residues: 385 sheet: -0.48 (0.80), residues: 40 loop : -0.74 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 168 HIS 0.003 0.000 HIS A 34 PHE 0.024 0.001 PHE B 374 TYR 0.010 0.001 TYR A 516 ARG 0.001 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 83 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 0.772 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 80 average time/residue: 0.1778 time to fit residues: 19.9893 Evaluate side-chains 80 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.722 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0702 time to fit residues: 1.4029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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: 0.7393 moved from start: 0.1535 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= 0.196 Angle : 0.508 6.522 9046 Z= 0.257 Chirality : 0.042 0.226 959 Planarity : 0.003 0.027 1166 Dihedral : 4.527 48.657 961 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.43 % Allowed : 25.07 % 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: 0.43 (0.31), residues: 786 helix: 1.35 (0.28), residues: 384 sheet: -0.61 (0.78), residues: 40 loop : -0.76 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 168 HIS 0.003 0.001 HIS A 34 PHE 0.023 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 86 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 0.722 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 84 average time/residue: 0.1707 time to fit residues: 20.1377 Evaluate side-chains 83 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.738 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0674 time to fit residues: 1.1999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 0.2980 chunk 54 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 0.1980 chunk 70 optimal weight: 0.3980 chunk 41 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.204699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.157806 restraints weight = 6665.425| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.90 r_work: 0.3319 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 6656 Z= 0.152 Angle : 0.485 6.197 9046 Z= 0.245 Chirality : 0.040 0.220 959 Planarity : 0.003 0.028 1166 Dihedral : 4.378 47.998 961 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.14 % Allowed : 25.79 % 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: 0.47 (0.31), residues: 786 helix: 1.40 (0.28), residues: 385 sheet: -0.56 (0.78), residues: 40 loop : -0.76 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 168 HIS 0.004 0.001 HIS A 34 PHE 0.019 0.001 PHE B 374 TYR 0.010 0.001 TYR A 516 ARG 0.001 0.000 ARG A 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1736.03 seconds wall clock time: 34 minutes 2.73 seconds (2042.73 seconds total)