Starting phenix.real_space_refine on Sun Mar 10 23:21:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw8_30230/03_2024/7bw8_30230.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw8_30230/03_2024/7bw8_30230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw8_30230/03_2024/7bw8_30230.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw8_30230/03_2024/7bw8_30230.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw8_30230/03_2024/7bw8_30230.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw8_30230/03_2024/7bw8_30230.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 46 5.16 5 C 3847 2.51 5 N 1026 2.21 5 O 1102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 6": "OE1" <-> "OE2" Residue "A ARG 19": "NH1" <-> "NH2" Residue "A PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 151": "OD1" <-> "OD2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A ASP 221": "OD1" <-> "OD2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 234": "OD1" <-> "OD2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 250": "OD1" <-> "OD2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A GLU 362": "OE1" <-> "OE2" Residue "A GLU 363": "OE1" <-> "OE2" Residue "A PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 404": "OD1" <-> "OD2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A ASP 456": "OD1" <-> "OD2" Residue "A ASP 464": "OD1" <-> "OD2" Residue "A PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 483": "OD1" <-> "OD2" Residue "A GLU 490": "OE1" <-> "OE2" Residue "A ASP 496": "OD1" <-> "OD2" Residue "A ASP 499": "OD1" <-> "OD2" Residue "A PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 509": "OE1" <-> "OE2" Residue "A PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 554": "NH1" <-> "NH2" Residue "A PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "A TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 584": "OD1" <-> "OD2" Residue "C TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 483": "OD1" <-> "OD2" Residue "C GLU 490": "OE1" <-> "OE2" Residue "C ASP 496": "OD1" <-> "OD2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 499": "OD1" <-> "OD2" Residue "C PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 517": "OE1" <-> "OE2" Residue "C ARG 554": "NH1" <-> "NH2" Residue "C ASP 574": "OD1" <-> "OD2" Residue "C TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 584": "OD1" <-> "OD2" Residue "C GLU 695": "OE1" <-> "OE2" Residue "C GLU 698": "OE1" <-> "OE2" Residue "C ASP 707": "OD1" <-> "OD2" Residue "C TYR 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 717": "NH1" <-> "NH2" Residue "D GLU 13": "OE1" <-> "OE2" Residue "D PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D GLU 72": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6021 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4469 Classifications: {'peptide': 551} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 525} Chain breaks: 3 Chain: "C" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1176 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain breaks: 2 Chain: "D" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Time building chain proxies: 3.80, per 1000 atoms: 0.63 Number of scatterers: 6021 At special positions: 0 Unit cell: (83.57, 94.53, 108.23, 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 46 16.00 O 1102 8.00 N 1026 7.00 C 3847 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.05 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.02 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.01 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.01 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.04 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=1.71 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.04 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.02 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 62 " distance=2.04 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 66 " 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 Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 1.3 seconds 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1398 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 11 sheets defined 15.2% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 16 through 20 removed outlier: 3.854A pdb=" N LEU A 20 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.625A pdb=" N ASP A 142 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.861A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N CYS A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 removed outlier: 3.656A pdb=" N GLY A 317 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 435 through 447 removed outlier: 4.108A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 removed outlier: 3.553A pdb=" N LEU A 500 " --> pdb=" O PHE A 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 697 Processing helix chain 'C' and resid 697 through 713 removed outlier: 4.209A pdb=" N LYS C 703 " --> pdb=" O SER C 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 19 removed outlier: 3.874A pdb=" N CYS D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 69 through 74 removed outlier: 3.944A pdb=" N ASN D 73 " --> pdb=" O TYR D 69 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14 removed outlier: 6.128A pdb=" N ILE A 13 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N MET A 38 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU A 63 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N MET A 98 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TYR A 67 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57 removed outlier: 3.625A pdb=" N ILE A 57 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE A 82 " --> pdb=" O ASN A 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA4, first strand: chain 'A' and resid 278 through 279 Processing sheet with id=AA5, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA6, first strand: chain 'A' and resid 335 through 336 removed outlier: 3.575A pdb=" N ILE A 336 " --> pdb=" O GLU A 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AA8, first strand: chain 'A' and resid 474 through 479 removed outlier: 6.233A pdb=" N PHE A 475 " --> pdb=" O GLU A 490 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU A 490 " --> pdb=" O PHE A 475 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 530 through 534 removed outlier: 3.750A pdb=" N THR A 530 " --> pdb=" O TYR A 507 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR A 507 " --> pdb=" O THR A 530 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR A 562 " --> pdb=" O VAL A 588 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 588 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL A 566 " --> pdb=" O ASP A 584 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ASP A 584 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N THR A 568 " --> pdb=" O LYS A 582 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LYS A 582 " --> pdb=" O THR A 568 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 485 through 486 removed outlier: 3.622A pdb=" N ILE C 485 " --> pdb=" O MET C 553 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 531 through 534 removed outlier: 3.574A pdb=" N VAL C 532 " --> pdb=" O LEU C 505 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR C 560 " --> pdb=" O THR C 590 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL C 566 " --> pdb=" O ASP C 584 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASP C 584 " --> pdb=" O VAL C 566 " (cutoff:3.500A) 101 hydrogen bonds defined for protein. 258 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: 1.43 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: 1478 1.33 - 1.46: 1574 1.46 - 1.58: 3063 1.58 - 1.71: 0 1.71 - 1.83: 57 Bond restraints: 6172 Sorted by residual: bond pdb=" N GLN A 589 " pdb=" CA GLN A 589 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.27e-02 6.20e+03 1.08e+01 bond pdb=" C PRO C 536 " pdb=" N PRO C 537 " ideal model delta sigma weight residual 1.335 1.307 0.028 8.70e-03 1.32e+04 1.04e+01 bond pdb=" N TYR A 477 " pdb=" CA TYR A 477 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.25e-02 6.40e+03 7.83e+00 bond pdb=" N VAL D 12 " pdb=" CA VAL D 12 " ideal model delta sigma weight residual 1.460 1.492 -0.033 1.21e-02 6.83e+03 7.33e+00 bond pdb=" N ARG A 252 " pdb=" CA ARG A 252 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.27e-02 6.20e+03 7.20e+00 ... (remaining 6167 not shown) Histogram of bond angle deviations from ideal: 99.47 - 106.43: 196 106.43 - 113.40: 3153 113.40 - 120.36: 2534 120.36 - 127.32: 2401 127.32 - 134.28: 79 Bond angle restraints: 8363 Sorted by residual: angle pdb=" N VAL A 445 " pdb=" CA VAL A 445 " pdb=" C VAL A 445 " ideal model delta sigma weight residual 112.29 108.64 3.65 9.40e-01 1.13e+00 1.51e+01 angle pdb=" N GLY C 555 " pdb=" CA GLY C 555 " pdb=" C GLY C 555 " ideal model delta sigma weight residual 113.18 122.28 -9.10 2.37e+00 1.78e-01 1.47e+01 angle pdb=" CA TYR D 16 " pdb=" CB TYR D 16 " pdb=" CG TYR D 16 " ideal model delta sigma weight residual 113.90 107.05 6.85 1.80e+00 3.09e-01 1.45e+01 angle pdb=" CA TRP C 559 " pdb=" C TRP C 559 " pdb=" O TRP C 559 " ideal model delta sigma weight residual 122.27 117.87 4.40 1.16e+00 7.43e-01 1.44e+01 angle pdb=" C THR C 560 " pdb=" N GLN C 561 " pdb=" CA GLN C 561 " ideal model delta sigma weight residual 120.87 126.15 -5.28 1.42e+00 4.96e-01 1.38e+01 ... (remaining 8358 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 3109 17.96 - 35.92: 482 35.92 - 53.88: 106 53.88 - 71.84: 13 71.84 - 89.80: 8 Dihedral angle restraints: 3718 sinusoidal: 1557 harmonic: 2161 Sorted by residual: dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 237 " pdb=" CB CYS A 237 " ideal model delta sinusoidal sigma weight residual 93.00 -178.14 -88.86 1 1.00e+01 1.00e-02 9.41e+01 dihedral pdb=" CB CYS D 61 " pdb=" SG CYS D 61 " pdb=" SG CYS D 66 " pdb=" CB CYS D 66 " ideal model delta sinusoidal sigma weight residual 93.00 6.87 86.13 1 1.00e+01 1.00e-02 8.95e+01 dihedral pdb=" CB CYS D 19 " pdb=" SG CYS D 19 " pdb=" SG CYS D 75 " pdb=" CB CYS D 75 " ideal model delta sinusoidal sigma weight residual 93.00 160.84 -67.84 1 1.00e+01 1.00e-02 5.98e+01 ... (remaining 3715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 574 0.059 - 0.118: 240 0.118 - 0.176: 74 0.176 - 0.235: 14 0.235 - 0.294: 3 Chirality restraints: 905 Sorted by residual: chirality pdb=" CB VAL A 515 " pdb=" CA VAL A 515 " pdb=" CG1 VAL A 515 " pdb=" CG2 VAL A 515 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA TYR D 16 " pdb=" N TYR D 16 " pdb=" C TYR D 16 " pdb=" CB TYR D 16 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA ASN A 541 " pdb=" N ASN A 541 " pdb=" C ASN A 541 " pdb=" CB ASN A 541 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 902 not shown) Planarity restraints: 1070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 16 " -0.036 2.00e-02 2.50e+03 3.14e-02 1.98e+01 pdb=" CG TYR D 16 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 TYR D 16 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR D 16 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR D 16 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR D 16 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR D 16 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 16 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 579 " 0.023 2.00e-02 2.50e+03 2.46e-02 1.21e+01 pdb=" CG TYR A 579 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR A 579 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 579 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR A 579 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR A 579 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 579 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 579 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 337 " -0.017 2.00e-02 2.50e+03 3.37e-02 1.13e+01 pdb=" CG ASN A 337 " 0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN A 337 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 337 " -0.020 2.00e-02 2.50e+03 ... (remaining 1067 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 164 2.56 - 3.14: 5673 3.14 - 3.73: 9188 3.73 - 4.31: 12124 4.31 - 4.90: 18616 Nonbonded interactions: 45765 Sorted by model distance: nonbonded pdb=" O SER A 540 " pdb=" OD1 ASN A 541 " model vdw 1.974 3.040 nonbonded pdb=" OD1 ASN A 541 " pdb=" OD1 ASP A 542 " model vdw 2.004 3.040 nonbonded pdb=" NZ LYS C 557 " pdb=" OG1 THR C 560 " model vdw 2.051 2.520 nonbonded pdb=" O GLU A 443 " pdb=" OG SER A 446 " model vdw 2.104 2.440 nonbonded pdb=" O THR A 571 " pdb=" OG1 THR A 578 " model vdw 2.109 2.440 ... (remaining 45760 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 group one per residue 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: 0.250 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: 1.100 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 19.400 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 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 : 0.009 0.087 6172 Z= 0.623 Angle : 1.376 12.295 8363 Z= 0.789 Chirality : 0.071 0.294 905 Planarity : 0.008 0.061 1070 Dihedral : 17.387 89.796 2275 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 49.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.25 % Favored : 77.75 % Rotamer: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -5.01 (0.26), residues: 719 helix: -2.92 (0.42), residues: 92 sheet: -2.21 (0.53), residues: 80 loop : -3.94 (0.23), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP A 183 HIS 0.022 0.004 HIS A 264 PHE 0.038 0.005 PHE A 231 TYR 0.077 0.005 TYR D 16 ARG 0.021 0.002 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8079 (mmt180) cc_final: 0.7387 (mmt90) REVERT: A 221 ASP cc_start: 0.7618 (m-30) cc_final: 0.7305 (p0) REVERT: A 310 LYS cc_start: 0.7883 (ttpp) cc_final: 0.7662 (pttp) REVERT: A 454 ARG cc_start: 0.7256 (mtt-85) cc_final: 0.6858 (mtt-85) REVERT: A 504 MET cc_start: 0.3325 (mmm) cc_final: 0.2903 (mmm) REVERT: A 553 MET cc_start: 0.8012 (mmm) cc_final: 0.7723 (mmm) REVERT: C 567 LYS cc_start: 0.3880 (mttm) cc_final: 0.2171 (ptmt) REVERT: C 695 GLU cc_start: 0.8748 (pm20) cc_final: 0.8295 (pm20) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.2207 time to fit residues: 43.5601 Evaluate side-chains 137 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 0.0370 chunk 18 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 34 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6172 Z= 0.263 Angle : 0.916 10.684 8363 Z= 0.463 Chirality : 0.053 0.226 905 Planarity : 0.006 0.069 1070 Dihedral : 7.695 28.354 805 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 26.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.72 % Favored : 84.28 % Rotamer: Outliers : 3.24 % Allowed : 16.22 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -4.60 (0.27), residues: 719 helix: -2.55 (0.44), residues: 96 sheet: -2.52 (0.44), residues: 106 loop : -3.55 (0.24), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 412 HIS 0.013 0.002 HIS A 264 PHE 0.016 0.002 PHE A 506 TYR 0.042 0.002 TYR D 16 ARG 0.009 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 166 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 11 MET cc_start: 0.6471 (pmm) cc_final: 0.6198 (pmm) REVERT: A 83 ARG cc_start: 0.7550 (mmt180) cc_final: 0.7254 (mmt90) REVERT: A 102 LYS cc_start: 0.8678 (pttm) cc_final: 0.8429 (mmtp) REVERT: A 379 LEU cc_start: 0.9598 (tp) cc_final: 0.9322 (tp) REVERT: A 383 ARG cc_start: 0.8305 (mtt180) cc_final: 0.7835 (mtm110) REVERT: A 553 MET cc_start: 0.7532 (mmm) cc_final: 0.7276 (mmm) REVERT: C 572 PHE cc_start: 0.8934 (m-80) cc_final: 0.8728 (m-80) REVERT: C 591 ASP cc_start: 0.5096 (t0) cc_final: 0.4681 (t0) REVERT: C 694 LYS cc_start: 0.7508 (mttp) cc_final: 0.7267 (ptpp) REVERT: D 13 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8235 (mt-10) REVERT: D 74 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.7198 (t80) outliers start: 22 outliers final: 15 residues processed: 175 average time/residue: 0.2028 time to fit residues: 45.0086 Evaluate side-chains 167 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 246 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 507 TYR Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 74 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 ASN C 711 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6172 Z= 0.222 Angle : 0.811 9.383 8363 Z= 0.409 Chirality : 0.050 0.216 905 Planarity : 0.006 0.062 1070 Dihedral : 6.969 26.110 805 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 23.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.02 % Favored : 84.98 % Rotamer: Outliers : 5.01 % Allowed : 21.24 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -4.21 (0.28), residues: 719 helix: -2.23 (0.47), residues: 96 sheet: -2.16 (0.48), residues: 100 loop : -3.31 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 412 HIS 0.009 0.001 HIS A 264 PHE 0.018 0.002 PHE A 428 TYR 0.034 0.002 TYR D 16 ARG 0.006 0.001 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 157 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.6595 (pmm) cc_final: 0.6254 (pmm) REVERT: A 83 ARG cc_start: 0.7444 (mmt180) cc_final: 0.7187 (mmt90) REVERT: A 383 ARG cc_start: 0.8389 (mtt180) cc_final: 0.7958 (mtm110) REVERT: A 465 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7294 (mp10) REVERT: A 500 LEU cc_start: 0.8147 (pp) cc_final: 0.7797 (tt) REVERT: A 553 MET cc_start: 0.7629 (mmm) cc_final: 0.7288 (mmm) REVERT: C 486 LEU cc_start: 0.8746 (tp) cc_final: 0.8516 (mp) REVERT: C 591 ASP cc_start: 0.4859 (t0) cc_final: 0.4392 (t0) REVERT: D 13 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8271 (mt-10) outliers start: 34 outliers final: 23 residues processed: 170 average time/residue: 0.2132 time to fit residues: 45.5420 Evaluate side-chains 168 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 246 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 507 TYR Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 27 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 0.3980 chunk 49 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 GLN ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6172 Z= 0.207 Angle : 0.777 8.923 8363 Z= 0.389 Chirality : 0.049 0.214 905 Planarity : 0.005 0.052 1070 Dihedral : 6.594 26.349 805 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 22.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.77 % Favored : 86.23 % Rotamer: Outliers : 5.46 % Allowed : 24.19 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -3.85 (0.29), residues: 719 helix: -1.90 (0.49), residues: 93 sheet: -2.03 (0.51), residues: 96 loop : -3.04 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 551 HIS 0.007 0.001 HIS D 10 PHE 0.014 0.002 PHE A 258 TYR 0.028 0.002 TYR D 16 ARG 0.009 0.001 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 154 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.6925 (pmm) cc_final: 0.6374 (pmm) REVERT: A 310 LYS cc_start: 0.7456 (tmmt) cc_final: 0.7232 (pttp) REVERT: A 383 ARG cc_start: 0.8352 (mtt180) cc_final: 0.7968 (mtm110) REVERT: A 465 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7304 (mp10) REVERT: A 500 LEU cc_start: 0.8237 (pp) cc_final: 0.7870 (tt) REVERT: C 591 ASP cc_start: 0.4745 (t0) cc_final: 0.4280 (t0) REVERT: D 76 ASN cc_start: 0.7916 (m110) cc_final: 0.7709 (m-40) outliers start: 37 outliers final: 29 residues processed: 172 average time/residue: 0.2063 time to fit residues: 45.0294 Evaluate side-chains 173 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 143 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 246 TYR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 507 TYR Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 579 TYR Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 27 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 0.2980 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6172 Z= 0.196 Angle : 0.763 10.109 8363 Z= 0.380 Chirality : 0.048 0.210 905 Planarity : 0.005 0.051 1070 Dihedral : 6.213 24.117 805 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.68 % Favored : 88.18 % Rotamer: Outliers : 5.31 % Allowed : 27.14 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -3.62 (0.29), residues: 719 helix: -1.68 (0.51), residues: 93 sheet: -1.93 (0.51), residues: 100 loop : -2.86 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 551 HIS 0.008 0.001 HIS D 10 PHE 0.014 0.001 PHE A 381 TYR 0.024 0.001 TYR D 16 ARG 0.005 0.001 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 149 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.6828 (pmm) cc_final: 0.6550 (pmm) REVERT: A 38 MET cc_start: 0.3556 (tpt) cc_final: 0.3199 (tpt) REVERT: A 313 HIS cc_start: 0.2920 (OUTLIER) cc_final: 0.1490 (m-70) REVERT: A 383 ARG cc_start: 0.8307 (mtt180) cc_final: 0.7948 (mtm110) REVERT: A 465 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7337 (mp10) REVERT: C 587 TYR cc_start: 0.6616 (OUTLIER) cc_final: 0.5835 (m-80) REVERT: C 591 ASP cc_start: 0.4581 (t0) cc_final: 0.4015 (t0) REVERT: C 694 LYS cc_start: 0.8124 (mptt) cc_final: 0.7789 (ptpp) outliers start: 36 outliers final: 27 residues processed: 167 average time/residue: 0.2117 time to fit residues: 45.0735 Evaluate side-chains 172 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 142 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 251 TRP Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 507 TYR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain C residue 572 PHE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 579 TYR Chi-restraints excluded: chain C residue 587 TYR Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 27 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 9.9990 chunk 62 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 32 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 GLN D 70 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6172 Z= 0.193 Angle : 0.763 11.211 8363 Z= 0.376 Chirality : 0.048 0.219 905 Planarity : 0.005 0.076 1070 Dihedral : 6.009 24.582 805 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.54 % Favored : 88.46 % Rotamer: Outliers : 6.64 % Allowed : 25.81 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -3.43 (0.30), residues: 719 helix: -1.62 (0.52), residues: 94 sheet: -1.66 (0.54), residues: 95 loop : -2.74 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 551 HIS 0.008 0.001 HIS D 10 PHE 0.013 0.001 PHE A 381 TYR 0.026 0.001 TYR D 16 ARG 0.009 0.001 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 144 time to evaluate : 0.731 Fit side-chains REVERT: A 11 MET cc_start: 0.6693 (pmm) cc_final: 0.6427 (pmm) REVERT: A 38 MET cc_start: 0.3579 (tpt) cc_final: 0.3345 (tpt) REVERT: A 86 ARG cc_start: 0.7698 (mtm110) cc_final: 0.7454 (mtp180) REVERT: A 265 LYS cc_start: 0.7421 (tmtt) cc_final: 0.7129 (tppt) REVERT: A 313 HIS cc_start: 0.2803 (OUTLIER) cc_final: 0.1089 (m-70) REVERT: A 331 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.7040 (mmt180) REVERT: A 383 ARG cc_start: 0.8313 (mtt180) cc_final: 0.7952 (mtm110) REVERT: A 465 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7345 (mp10) REVERT: A 514 ASN cc_start: 0.8179 (OUTLIER) cc_final: 0.7977 (m-40) REVERT: C 551 TRP cc_start: 0.7318 (t-100) cc_final: 0.6994 (t-100) REVERT: C 587 TYR cc_start: 0.6662 (OUTLIER) cc_final: 0.5708 (m-80) REVERT: C 591 ASP cc_start: 0.4542 (t0) cc_final: 0.4001 (t0) REVERT: C 694 LYS cc_start: 0.8123 (mptt) cc_final: 0.7805 (ptpp) REVERT: D 13 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8279 (mt-10) outliers start: 45 outliers final: 32 residues processed: 170 average time/residue: 0.2069 time to fit residues: 44.1345 Evaluate side-chains 174 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 137 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 507 TYR Chi-restraints excluded: chain A residue 514 ASN Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 572 PHE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 579 TYR Chi-restraints excluded: chain C residue 587 TYR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 27 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 50 optimal weight: 0.0070 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 43 optimal weight: 0.0040 chunk 42 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 30.0000 chunk 41 optimal weight: 0.9980 overall best weight: 0.4610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6172 Z= 0.180 Angle : 0.767 9.929 8363 Z= 0.372 Chirality : 0.048 0.205 905 Planarity : 0.005 0.051 1070 Dihedral : 5.761 21.697 805 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.54 % Favored : 88.46 % Rotamer: Outliers : 6.05 % Allowed : 26.99 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -3.11 (0.31), residues: 719 helix: -1.71 (0.54), residues: 90 sheet: -1.35 (0.59), residues: 87 loop : -2.45 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 551 HIS 0.008 0.001 HIS D 10 PHE 0.022 0.001 PHE A 39 TYR 0.013 0.001 TYR A 512 ARG 0.007 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 145 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.6626 (pmm) cc_final: 0.6320 (pmm) REVERT: A 34 GLN cc_start: 0.6963 (mm-40) cc_final: 0.6748 (mm-40) REVERT: A 38 MET cc_start: 0.3714 (tpt) cc_final: 0.3436 (tpt) REVERT: A 83 ARG cc_start: 0.7041 (mmt90) cc_final: 0.6799 (mmt90) REVERT: A 86 ARG cc_start: 0.7652 (mtm110) cc_final: 0.7411 (mtp180) REVERT: A 260 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8361 (tm-30) REVERT: A 313 HIS cc_start: 0.2887 (OUTLIER) cc_final: 0.1136 (m-70) REVERT: A 383 ARG cc_start: 0.8318 (mtt180) cc_final: 0.7956 (mtm110) REVERT: A 465 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7262 (mp10) REVERT: A 560 THR cc_start: 0.3383 (OUTLIER) cc_final: 0.2768 (p) REVERT: C 478 ILE cc_start: 0.8482 (tp) cc_final: 0.8246 (mp) REVERT: C 551 TRP cc_start: 0.7226 (t-100) cc_final: 0.6908 (t-100) REVERT: C 567 LYS cc_start: 0.3247 (ttmt) cc_final: 0.2888 (tttt) REVERT: C 587 TYR cc_start: 0.6616 (OUTLIER) cc_final: 0.5657 (m-80) REVERT: C 591 ASP cc_start: 0.5150 (t0) cc_final: 0.4605 (t0) REVERT: D 74 TYR cc_start: 0.6965 (m-80) cc_final: 0.6729 (m-80) outliers start: 41 outliers final: 25 residues processed: 167 average time/residue: 0.1992 time to fit residues: 42.4429 Evaluate side-chains 166 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 507 TYR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 579 TYR Chi-restraints excluded: chain C residue 587 TYR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 76 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 44 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 54 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 60 optimal weight: 0.0050 chunk 64 optimal weight: 7.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6172 Z= 0.193 Angle : 0.767 9.934 8363 Z= 0.377 Chirality : 0.048 0.211 905 Planarity : 0.005 0.076 1070 Dihedral : 5.856 25.128 805 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.96 % Favored : 87.90 % Rotamer: Outliers : 6.05 % Allowed : 27.58 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -3.10 (0.31), residues: 719 helix: -1.87 (0.53), residues: 90 sheet: -1.36 (0.59), residues: 87 loop : -2.41 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 551 HIS 0.008 0.001 HIS D 10 PHE 0.020 0.001 PHE A 39 TYR 0.026 0.001 TYR C 507 ARG 0.006 0.001 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 140 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.6619 (pmm) cc_final: 0.6301 (pmm) REVERT: A 86 ARG cc_start: 0.7649 (mtm110) cc_final: 0.7423 (mtp180) REVERT: A 125 LEU cc_start: 0.8593 (mt) cc_final: 0.8362 (mt) REVERT: A 265 LYS cc_start: 0.7453 (tmtt) cc_final: 0.7149 (tppt) REVERT: A 313 HIS cc_start: 0.2934 (OUTLIER) cc_final: 0.1187 (m-70) REVERT: A 383 ARG cc_start: 0.8348 (mtt180) cc_final: 0.7986 (mtm110) REVERT: A 465 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7470 (mp10) REVERT: A 500 LEU cc_start: 0.7943 (pp) cc_final: 0.7491 (tt) REVERT: A 560 THR cc_start: 0.3477 (OUTLIER) cc_final: 0.2834 (p) REVERT: C 478 ILE cc_start: 0.8606 (tp) cc_final: 0.8367 (mp) REVERT: C 551 TRP cc_start: 0.7241 (t-100) cc_final: 0.6928 (t-100) REVERT: C 587 TYR cc_start: 0.6627 (OUTLIER) cc_final: 0.5650 (m-80) REVERT: C 591 ASP cc_start: 0.5277 (t0) cc_final: 0.4700 (t0) outliers start: 41 outliers final: 34 residues processed: 166 average time/residue: 0.1883 time to fit residues: 40.4100 Evaluate side-chains 174 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 136 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 251 TRP Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 507 TYR Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 591 ASP Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 572 PHE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 579 TYR Chi-restraints excluded: chain C residue 587 TYR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 61 optimal weight: 0.0170 chunk 64 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 overall best weight: 1.9224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6172 Z= 0.283 Angle : 0.838 10.204 8363 Z= 0.417 Chirality : 0.051 0.196 905 Planarity : 0.005 0.050 1070 Dihedral : 6.259 33.008 805 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 26.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.60 % Favored : 85.40 % Rotamer: Outliers : 5.90 % Allowed : 28.02 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.40 (0.30), residues: 719 helix: -2.06 (0.50), residues: 93 sheet: -1.32 (0.61), residues: 79 loop : -2.67 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 133 HIS 0.009 0.002 HIS D 10 PHE 0.016 0.002 PHE A 39 TYR 0.026 0.002 TYR A 91 ARG 0.010 0.001 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 149 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.6689 (pmm) cc_final: 0.6311 (pmm) REVERT: A 98 MET cc_start: 0.6203 (tpp) cc_final: 0.5882 (tpp) REVERT: A 125 LEU cc_start: 0.8610 (mt) cc_final: 0.8394 (mt) REVERT: A 189 GLN cc_start: 0.6405 (OUTLIER) cc_final: 0.6029 (mt0) REVERT: A 260 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8480 (tm-30) REVERT: A 313 HIS cc_start: 0.3082 (OUTLIER) cc_final: 0.2719 (t-90) REVERT: A 383 ARG cc_start: 0.8376 (mtt180) cc_final: 0.7985 (mtm110) REVERT: A 386 ARG cc_start: 0.7816 (mtt180) cc_final: 0.7605 (mtt180) REVERT: A 465 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7599 (mp10) REVERT: A 500 LEU cc_start: 0.8082 (pp) cc_final: 0.7674 (tt) REVERT: A 504 MET cc_start: 0.3990 (mmm) cc_final: 0.2968 (mmm) REVERT: C 486 LEU cc_start: 0.8927 (mp) cc_final: 0.8722 (mp) REVERT: C 488 ARG cc_start: 0.8230 (tpt170) cc_final: 0.7776 (ttt90) REVERT: C 551 TRP cc_start: 0.7416 (t-100) cc_final: 0.7131 (t-100) REVERT: C 587 TYR cc_start: 0.6648 (OUTLIER) cc_final: 0.6052 (m-80) REVERT: C 591 ASP cc_start: 0.5542 (t0) cc_final: 0.5027 (t0) outliers start: 40 outliers final: 31 residues processed: 172 average time/residue: 0.2126 time to fit residues: 45.9319 Evaluate side-chains 175 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 140 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 507 TYR Chi-restraints excluded: chain A residue 514 ASN Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 572 PHE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 579 TYR Chi-restraints excluded: chain C residue 587 TYR Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 0.0060 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6172 Z= 0.201 Angle : 0.821 10.459 8363 Z= 0.399 Chirality : 0.049 0.206 905 Planarity : 0.005 0.074 1070 Dihedral : 6.004 24.771 805 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.40 % Favored : 88.46 % Rotamer: Outliers : 4.28 % Allowed : 30.09 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -3.12 (0.30), residues: 719 helix: -2.02 (0.52), residues: 91 sheet: -1.42 (0.57), residues: 87 loop : -2.39 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 551 HIS 0.007 0.001 HIS D 10 PHE 0.017 0.001 PHE A 39 TYR 0.023 0.001 TYR C 507 ARG 0.008 0.001 ARG A 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 142 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.6591 (pmm) cc_final: 0.6269 (pmm) REVERT: A 38 MET cc_start: 0.4057 (tpt) cc_final: 0.3812 (tpt) REVERT: A 98 MET cc_start: 0.6151 (tpp) cc_final: 0.5911 (tpp) REVERT: A 125 LEU cc_start: 0.8207 (mt) cc_final: 0.7923 (mt) REVERT: A 265 LYS cc_start: 0.7422 (tmtt) cc_final: 0.7154 (tppt) REVERT: A 313 HIS cc_start: 0.2942 (OUTLIER) cc_final: 0.2521 (t-90) REVERT: A 383 ARG cc_start: 0.8371 (mtt180) cc_final: 0.7996 (mtm110) REVERT: A 465 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7476 (mp10) REVERT: A 500 LEU cc_start: 0.7996 (pp) cc_final: 0.7677 (tt) REVERT: A 504 MET cc_start: 0.4204 (mmm) cc_final: 0.3215 (mmm) REVERT: C 488 ARG cc_start: 0.8000 (tpt170) cc_final: 0.7630 (ttt90) REVERT: C 551 TRP cc_start: 0.7364 (t-100) cc_final: 0.6988 (t-100) REVERT: C 587 TYR cc_start: 0.6611 (OUTLIER) cc_final: 0.5621 (m-80) REVERT: C 591 ASP cc_start: 0.5496 (t0) cc_final: 0.5000 (t0) outliers start: 29 outliers final: 24 residues processed: 159 average time/residue: 0.2209 time to fit residues: 44.0777 Evaluate side-chains 161 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 134 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 507 TYR Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 579 TYR Chi-restraints excluded: chain C residue 587 TYR Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 27 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 58 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 50 optimal weight: 0.0000 chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.168508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.149667 restraints weight = 15845.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.154015 restraints weight = 9736.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.156755 restraints weight = 5848.432| |-----------------------------------------------------------------------------| r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6172 Z= 0.195 Angle : 0.799 10.216 8363 Z= 0.386 Chirality : 0.048 0.210 905 Planarity : 0.005 0.082 1070 Dihedral : 5.783 22.736 805 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.10 % Favored : 87.76 % Rotamer: Outliers : 4.28 % Allowed : 30.38 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -3.01 (0.30), residues: 719 helix: -1.81 (0.54), residues: 89 sheet: -1.29 (0.58), residues: 87 loop : -2.34 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 551 HIS 0.007 0.001 HIS D 10 PHE 0.015 0.001 PHE A 39 TYR 0.015 0.001 TYR C 492 ARG 0.007 0.001 ARG A 409 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1763.17 seconds wall clock time: 32 minutes 36.25 seconds (1956.25 seconds total)