Starting phenix.real_space_refine on Sat Aug 3 01:15:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc5_39923/08_2024/8zc5_39923.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc5_39923/08_2024/8zc5_39923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc5_39923/08_2024/8zc5_39923.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc5_39923/08_2024/8zc5_39923.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc5_39923/08_2024/8zc5_39923.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc5_39923/08_2024/8zc5_39923.cif" } resolution = 3.91 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= 0.026 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 32 5.16 5 C 4150 2.51 5 N 1102 2.21 5 O 1231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 442": "OD1" <-> "OD2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 46": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6515 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1562 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 12, 'TRANS': 183} Chain: "B" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1359 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 9, 'TRANS': 158} Chain breaks: 2 Chain: "C" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 810 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "D" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 810 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "E" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 973 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "F" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 973 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "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: 4.33, per 1000 atoms: 0.66 Number of scatterers: 6515 At special positions: 0 Unit cell: (111.232, 94.336, 116.864, 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 32 16.00 O 1231 8.00 N 1102 7.00 C 4150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.05 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 103 " - pdb=" SG CYS E 108 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 103 " - pdb=" SG CYS F 108 " 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 601 " - " ASN A 343 " " NAG B 601 " - " ASN B 343 " Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.2 seconds 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1518 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 18 sheets defined 8.9% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.707A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.554A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.579A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.733A pdb=" N ASN B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 339 through 343' Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.152A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.590A pdb=" N ASP E 31 " --> pdb=" O ILE E 28 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.881A pdb=" N GLN E 65 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.682A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 112 removed outlier: 3.572A pdb=" N TRP E 111 " --> pdb=" O CYS E 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.957A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 112 removed outlier: 3.541A pdb=" N TRP F 111 " --> pdb=" O CYS F 108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.698A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.667A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL B 433 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE B 377 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA B 435 " --> pdb=" O PHE B 375 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.557A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.568A pdb=" N ALA C 10 " --> pdb=" O LYS C 106 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR C 108 " --> pdb=" O ALA C 10 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY C 12 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.568A pdb=" N ALA C 10 " --> pdb=" O LYS C 106 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR C 108 " --> pdb=" O ALA C 10 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY C 12 " --> pdb=" O THR C 108 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 17 through 23 Processing sheet with id=AB1, first strand: chain 'D' and resid 9 through 10 Processing sheet with id=AB2, first strand: chain 'D' and resid 17 through 22 Processing sheet with id=AB3, first strand: chain 'D' and resid 45 through 49 removed outlier: 6.499A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP D 86 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP D 93 " --> pdb=" O GLY D 98 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY D 98 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.592A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL E 20 " --> pdb=" O MET E 81 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.600A pdb=" N THR E 116 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.619A pdb=" N TYR E 94 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA E 121 " --> pdb=" O TYR E 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.697A pdb=" N VAL F 5 " --> pdb=" O LYS F 23 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 58 through 59 removed outlier: 3.505A pdb=" N ASN F 59 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP F 50 " --> pdb=" O ASN F 59 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TRP F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN F 33 " --> pdb=" O SER F 99 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ARG F 98 " --> pdb=" O ASP F 115 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 58 through 59 removed outlier: 3.505A pdb=" N ASN F 59 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP F 50 " --> pdb=" O ASN F 59 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TRP F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN F 33 " --> pdb=" O SER F 99 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA F 121 " --> pdb=" O TYR F 94 " (cutoff:3.500A) 178 hydrogen bonds defined for protein. 444 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: 1.84 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2045 1.34 - 1.46: 1458 1.46 - 1.58: 3152 1.58 - 1.70: 0 1.70 - 1.82: 40 Bond restraints: 6695 Sorted by residual: bond pdb=" CA CYS A 480 " pdb=" C CYS A 480 " ideal model delta sigma weight residual 1.524 1.497 0.027 1.29e-02 6.01e+03 4.23e+00 bond pdb=" C PHE B 342 " pdb=" N ASN B 343 " ideal model delta sigma weight residual 1.331 1.304 0.026 1.48e-02 4.57e+03 3.21e+00 bond pdb=" C CYS A 480 " pdb=" N ASN A 481 " ideal model delta sigma weight residual 1.332 1.308 0.025 1.40e-02 5.10e+03 3.13e+00 bond pdb=" CA ASN B 343 " pdb=" C ASN B 343 " ideal model delta sigma weight residual 1.523 1.498 0.024 1.41e-02 5.03e+03 2.96e+00 bond pdb=" N CYS A 480 " pdb=" CA CYS A 480 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.23e-02 6.61e+03 2.58e+00 ... (remaining 6690 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.57: 216 106.57 - 113.42: 3393 113.42 - 120.27: 2372 120.27 - 127.12: 3032 127.12 - 133.97: 91 Bond angle restraints: 9104 Sorted by residual: angle pdb=" C CYS A 480 " pdb=" N ASN A 481 " pdb=" CA ASN A 481 " ideal model delta sigma weight residual 122.07 127.76 -5.69 1.43e+00 4.89e-01 1.58e+01 angle pdb=" C ILE E 76 " pdb=" N THR E 77 " pdb=" CA THR E 77 " ideal model delta sigma weight residual 121.54 129.08 -7.54 1.91e+00 2.74e-01 1.56e+01 angle pdb=" N THR D 31 " pdb=" CA THR D 31 " pdb=" C THR D 31 " ideal model delta sigma weight residual 113.18 108.06 5.12 1.33e+00 5.65e-01 1.48e+01 angle pdb=" CB MET F 112 " pdb=" CG MET F 112 " pdb=" SD MET F 112 " ideal model delta sigma weight residual 112.70 123.65 -10.95 3.00e+00 1.11e-01 1.33e+01 angle pdb=" C LYS D 51 " pdb=" N ASN D 52 " pdb=" CA ASN D 52 " ideal model delta sigma weight residual 121.54 128.34 -6.80 1.91e+00 2.74e-01 1.27e+01 ... (remaining 9099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.97: 3497 15.97 - 31.93: 359 31.93 - 47.90: 68 47.90 - 63.87: 10 63.87 - 79.83: 11 Dihedral angle restraints: 3945 sinusoidal: 1554 harmonic: 2391 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 13.17 79.83 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual -86.00 -138.08 52.08 1 1.00e+01 1.00e-02 3.70e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -137.53 51.53 1 1.00e+01 1.00e-02 3.63e+01 ... (remaining 3942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 592 0.042 - 0.083: 262 0.083 - 0.124: 88 0.124 - 0.166: 18 0.166 - 0.207: 4 Chirality restraints: 964 Sorted by residual: chirality pdb=" CA ASN A 481 " pdb=" N ASN A 481 " pdb=" C ASN A 481 " pdb=" CB ASN A 481 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA THR E 77 " pdb=" N THR E 77 " pdb=" C THR E 77 " pdb=" CB THR E 77 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CB VAL A 367 " pdb=" CA VAL A 367 " pdb=" CG1 VAL A 367 " pdb=" CG2 VAL A 367 " both_signs ideal model delta sigma weight residual False -2.63 -2.80 0.18 2.00e-01 2.50e+01 7.68e-01 ... (remaining 961 not shown) Planarity restraints: 1178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 601 " -0.132 2.00e-02 2.50e+03 1.10e-01 1.51e+02 pdb=" C7 NAG B 601 " 0.036 2.00e-02 2.50e+03 pdb=" C8 NAG B 601 " -0.098 2.00e-02 2.50e+03 pdb=" N2 NAG B 601 " 0.178 2.00e-02 2.50e+03 pdb=" O7 NAG B 601 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 601 " 0.044 2.00e-02 2.50e+03 3.62e-02 1.64e+01 pdb=" C7 NAG A 601 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG A 601 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG A 601 " -0.057 2.00e-02 2.50e+03 pdb=" O7 NAG A 601 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 480 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.24e+00 pdb=" C CYS A 480 " -0.040 2.00e-02 2.50e+03 pdb=" O CYS A 480 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN A 481 " 0.014 2.00e-02 2.50e+03 ... (remaining 1175 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1484 2.79 - 3.31: 5404 3.31 - 3.84: 10277 3.84 - 4.37: 11329 4.37 - 4.90: 20499 Nonbonded interactions: 48993 Sorted by model distance: nonbonded pdb=" OE1 GLN D 6 " pdb=" OG1 THR D 105 " model vdw 2.258 3.040 nonbonded pdb=" OG SER A 443 " pdb=" O PHE A 497 " model vdw 2.267 3.040 nonbonded pdb=" O CYS A 480 " pdb=" OD1 ASN A 481 " model vdw 2.273 3.040 nonbonded pdb=" OG SER A 359 " pdb=" OD1 ASN A 394 " model vdw 2.280 3.040 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.295 3.040 ... (remaining 48988 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 338 through 359 or resid 367 through 390 or resid 394 thro \ ugh 515 or resid 601)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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=0.00 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: 1.690 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 21.680 Find NCS groups from input model: 0.230 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 0.041 6695 Z= 0.250 Angle : 0.755 10.951 9104 Z= 0.405 Chirality : 0.051 0.207 964 Planarity : 0.006 0.110 1176 Dihedral : 13.545 79.536 2391 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.28), residues: 814 helix: -4.45 (0.61), residues: 14 sheet: -0.13 (0.32), residues: 257 loop : -1.46 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 50 HIS 0.003 0.001 HIS E 35 PHE 0.037 0.002 PHE A 456 TYR 0.030 0.002 TYR A 495 ARG 0.015 0.001 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: B 467 ASP cc_start: 0.8247 (p0) cc_final: 0.7961 (p0) REVERT: D 6 GLN cc_start: 0.8499 (pt0) cc_final: 0.7664 (pt0) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2001 time to fit residues: 43.4758 Evaluate side-chains 136 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.8980 chunk 59 optimal weight: 0.0970 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN D 6 GLN D 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6695 Z= 0.268 Angle : 0.608 9.636 9104 Z= 0.316 Chirality : 0.047 0.156 964 Planarity : 0.004 0.035 1176 Dihedral : 4.729 25.059 955 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.57 % Allowed : 11.54 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.29), residues: 814 helix: -3.68 (0.81), residues: 20 sheet: 0.10 (0.30), residues: 268 loop : -1.21 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 36 HIS 0.003 0.001 HIS E 35 PHE 0.029 0.002 PHE F 29 TYR 0.017 0.001 TYR A 495 ARG 0.006 0.000 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: B 467 ASP cc_start: 0.8264 (p0) cc_final: 0.7891 (p0) REVERT: C 47 LEU cc_start: 0.8071 (tp) cc_final: 0.7810 (tp) REVERT: D 6 GLN cc_start: 0.8539 (pt0) cc_final: 0.7701 (pt0) REVERT: F 39 GLN cc_start: 0.7744 (tp40) cc_final: 0.7515 (tp40) outliers start: 4 outliers final: 3 residues processed: 144 average time/residue: 0.1944 time to fit residues: 36.4028 Evaluate side-chains 138 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain F residue 70 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 0.0010 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 19 optimal weight: 0.0870 chunk 71 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 477 ASN D 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6695 Z= 0.191 Angle : 0.569 7.863 9104 Z= 0.290 Chirality : 0.045 0.150 964 Planarity : 0.004 0.034 1176 Dihedral : 4.454 21.049 955 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.00 % Allowed : 13.96 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.29), residues: 814 helix: -3.79 (0.76), residues: 20 sheet: 0.11 (0.30), residues: 274 loop : -1.09 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 50 HIS 0.003 0.001 HIS E 35 PHE 0.017 0.001 PHE A 400 TYR 0.014 0.001 TYR A 495 ARG 0.006 0.000 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8280 (m-40) cc_final: 0.7888 (t0) REVERT: B 467 ASP cc_start: 0.8249 (p0) cc_final: 0.7865 (p0) REVERT: D 6 GLN cc_start: 0.8528 (pt0) cc_final: 0.7926 (pt0) REVERT: F 39 GLN cc_start: 0.7545 (tp40) cc_final: 0.7230 (tp40) outliers start: 7 outliers final: 4 residues processed: 139 average time/residue: 0.2021 time to fit residues: 36.1648 Evaluate side-chains 134 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 130 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 83 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6695 Z= 0.251 Angle : 0.575 8.567 9104 Z= 0.294 Chirality : 0.045 0.148 964 Planarity : 0.004 0.036 1176 Dihedral : 4.439 16.986 955 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.57 % Allowed : 14.39 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.30), residues: 814 helix: -3.77 (0.78), residues: 20 sheet: -0.07 (0.30), residues: 284 loop : -0.99 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 50 HIS 0.004 0.001 HIS E 35 PHE 0.018 0.001 PHE B 400 TYR 0.018 0.001 TYR A 495 ARG 0.007 0.000 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 136 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8355 (m-40) cc_final: 0.7922 (t0) REVERT: B 467 ASP cc_start: 0.8282 (p0) cc_final: 0.7878 (p0) REVERT: B 498 ARG cc_start: 0.8593 (mtt-85) cc_final: 0.7910 (mtt-85) REVERT: D 6 GLN cc_start: 0.8579 (pt0) cc_final: 0.8029 (pt0) REVERT: F 39 GLN cc_start: 0.7528 (tp40) cc_final: 0.7304 (tp40) REVERT: F 119 GLN cc_start: 0.8014 (mp10) cc_final: 0.7726 (mp10) outliers start: 11 outliers final: 9 residues processed: 143 average time/residue: 0.2070 time to fit residues: 38.0811 Evaluate side-chains 137 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 124 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 19 optimal weight: 0.0000 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6695 Z= 0.214 Angle : 0.563 9.531 9104 Z= 0.285 Chirality : 0.045 0.143 964 Planarity : 0.004 0.037 1176 Dihedral : 4.350 17.710 955 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.57 % Allowed : 16.24 % Favored : 82.19 % 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: -0.98 (0.30), residues: 814 helix: -3.77 (0.76), residues: 20 sheet: 0.15 (0.31), residues: 270 loop : -0.99 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 50 HIS 0.003 0.001 HIS E 35 PHE 0.016 0.001 PHE A 400 TYR 0.015 0.001 TYR B 453 ARG 0.007 0.000 ARG C 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8377 (m-40) cc_final: 0.8122 (t0) REVERT: B 467 ASP cc_start: 0.8287 (p0) cc_final: 0.7905 (p0) REVERT: B 498 ARG cc_start: 0.8525 (mtt-85) cc_final: 0.7928 (mtt-85) REVERT: D 6 GLN cc_start: 0.8626 (pt0) cc_final: 0.8065 (pt0) REVERT: F 39 GLN cc_start: 0.7387 (tp40) cc_final: 0.7186 (tp40) REVERT: F 119 GLN cc_start: 0.8251 (mp10) cc_final: 0.7938 (mp10) outliers start: 11 outliers final: 7 residues processed: 141 average time/residue: 0.2063 time to fit residues: 37.4991 Evaluate side-chains 137 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 124 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6695 Z= 0.270 Angle : 0.607 10.614 9104 Z= 0.302 Chirality : 0.045 0.149 964 Planarity : 0.004 0.042 1176 Dihedral : 4.417 18.330 955 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.99 % Allowed : 16.38 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.30), residues: 814 helix: -3.82 (0.76), residues: 20 sheet: -0.13 (0.30), residues: 284 loop : -0.91 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 50 HIS 0.004 0.001 HIS E 35 PHE 0.017 0.001 PHE A 400 TYR 0.017 0.001 TYR A 495 ARG 0.009 0.000 ARG C 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: B 467 ASP cc_start: 0.8301 (p0) cc_final: 0.7925 (p0) REVERT: B 498 ARG cc_start: 0.8636 (mtt-85) cc_final: 0.8083 (mtt-85) REVERT: D 6 GLN cc_start: 0.8641 (pt0) cc_final: 0.8146 (pt0) REVERT: F 119 GLN cc_start: 0.8234 (mp10) cc_final: 0.7931 (mp10) outliers start: 14 outliers final: 10 residues processed: 142 average time/residue: 0.2037 time to fit residues: 37.5916 Evaluate side-chains 136 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 124 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 0.0870 chunk 46 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 0.0470 chunk 45 optimal weight: 0.8980 chunk 22 optimal weight: 0.0670 chunk 14 optimal weight: 0.9990 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN D 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6695 Z= 0.186 Angle : 0.601 10.862 9104 Z= 0.295 Chirality : 0.045 0.143 964 Planarity : 0.003 0.039 1176 Dihedral : 4.324 19.670 955 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.57 % Allowed : 18.23 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.30), residues: 814 helix: -4.13 (0.60), residues: 26 sheet: 0.05 (0.30), residues: 274 loop : -0.98 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 50 HIS 0.003 0.000 HIS E 35 PHE 0.015 0.001 PHE A 400 TYR 0.014 0.001 TYR B 453 ARG 0.008 0.000 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: A 429 PHE cc_start: 0.7600 (t80) cc_final: 0.7382 (t80) REVERT: B 386 LYS cc_start: 0.5156 (pttt) cc_final: 0.4035 (tttt) REVERT: B 467 ASP cc_start: 0.8276 (p0) cc_final: 0.7914 (p0) REVERT: B 498 ARG cc_start: 0.8590 (mtt-85) cc_final: 0.8064 (mtt-85) REVERT: D 6 GLN cc_start: 0.8654 (pt0) cc_final: 0.8136 (pt0) REVERT: F 119 GLN cc_start: 0.8222 (mp10) cc_final: 0.7960 (mp10) outliers start: 11 outliers final: 9 residues processed: 143 average time/residue: 0.2053 time to fit residues: 37.7730 Evaluate side-chains 141 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 132 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 124 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 chunk 69 optimal weight: 0.8980 chunk 72 optimal weight: 0.3980 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6695 Z= 0.242 Angle : 0.611 10.919 9104 Z= 0.303 Chirality : 0.045 0.151 964 Planarity : 0.003 0.039 1176 Dihedral : 4.380 18.135 955 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.85 % Allowed : 17.95 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.30), residues: 814 helix: -3.86 (0.75), residues: 20 sheet: 0.03 (0.31), residues: 272 loop : -0.92 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 50 HIS 0.004 0.001 HIS E 35 PHE 0.016 0.001 PHE A 400 TYR 0.016 0.001 TYR B 453 ARG 0.007 0.000 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 137 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 429 PHE cc_start: 0.7626 (t80) cc_final: 0.7384 (t80) REVERT: B 386 LYS cc_start: 0.4997 (pttt) cc_final: 0.3882 (tttt) REVERT: B 467 ASP cc_start: 0.8290 (p0) cc_final: 0.7929 (p0) REVERT: B 498 ARG cc_start: 0.8637 (mtt-85) cc_final: 0.8032 (mtt-85) REVERT: D 6 GLN cc_start: 0.8680 (pt0) cc_final: 0.8168 (pt0) REVERT: F 4 LEU cc_start: 0.8269 (tp) cc_final: 0.8005 (tp) REVERT: F 67 ARG cc_start: 0.6711 (mtm-85) cc_final: 0.6356 (mtm-85) REVERT: F 119 GLN cc_start: 0.8252 (mp10) cc_final: 0.8008 (mp10) outliers start: 13 outliers final: 13 residues processed: 146 average time/residue: 0.2059 time to fit residues: 38.5986 Evaluate side-chains 142 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 21 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 0.0060 chunk 64 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 46 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 45 optimal weight: 0.0000 chunk 35 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6695 Z= 0.202 Angle : 0.606 10.760 9104 Z= 0.301 Chirality : 0.045 0.152 964 Planarity : 0.003 0.039 1176 Dihedral : 4.315 19.084 955 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.85 % Allowed : 18.52 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.30), residues: 814 helix: -3.90 (0.76), residues: 20 sheet: 0.05 (0.30), residues: 272 loop : -0.89 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 50 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE A 400 TYR 0.015 0.001 TYR B 453 ARG 0.007 0.000 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 137 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.7605 (t80) cc_final: 0.7366 (t80) REVERT: B 467 ASP cc_start: 0.8281 (p0) cc_final: 0.7908 (p0) REVERT: B 498 ARG cc_start: 0.8588 (mtt-85) cc_final: 0.8019 (mtt-85) REVERT: D 6 GLN cc_start: 0.8677 (pt0) cc_final: 0.8157 (pt0) REVERT: F 4 LEU cc_start: 0.8307 (tp) cc_final: 0.8045 (tp) REVERT: F 67 ARG cc_start: 0.6727 (mtm-85) cc_final: 0.6352 (mtm-85) REVERT: F 119 GLN cc_start: 0.8258 (mp10) cc_final: 0.8046 (mp10) outliers start: 13 outliers final: 12 residues processed: 144 average time/residue: 0.2064 time to fit residues: 38.1047 Evaluate side-chains 142 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 130 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 0.8980 chunk 72 optimal weight: 0.2980 chunk 62 optimal weight: 0.1980 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 66 optimal weight: 0.0060 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6695 Z= 0.206 Angle : 0.617 10.933 9104 Z= 0.305 Chirality : 0.045 0.148 964 Planarity : 0.003 0.039 1176 Dihedral : 4.284 20.454 955 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.71 % Allowed : 19.23 % Favored : 79.06 % 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: -0.93 (0.30), residues: 814 helix: -3.95 (0.76), residues: 20 sheet: 0.06 (0.30), residues: 272 loop : -0.86 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 50 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE A 400 TYR 0.015 0.001 TYR B 453 ARG 0.007 0.000 ARG D 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 130 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: A 429 PHE cc_start: 0.7598 (t80) cc_final: 0.7357 (t80) REVERT: B 386 LYS cc_start: 0.5184 (pttt) cc_final: 0.4072 (tttt) REVERT: B 467 ASP cc_start: 0.8270 (p0) cc_final: 0.7907 (p0) REVERT: B 498 ARG cc_start: 0.8584 (mtt-85) cc_final: 0.8006 (mtt-85) REVERT: D 6 GLN cc_start: 0.8643 (pt0) cc_final: 0.8221 (pt0) REVERT: F 67 ARG cc_start: 0.6843 (mtm-85) cc_final: 0.6489 (mtm-85) outliers start: 12 outliers final: 12 residues processed: 138 average time/residue: 0.2301 time to fit residues: 40.6700 Evaluate side-chains 141 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 chunk 26 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 45 optimal weight: 0.0770 chunk 71 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.165989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.136991 restraints weight = 8790.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.134591 restraints weight = 11849.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.136762 restraints weight = 10780.890| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6695 Z= 0.205 Angle : 0.626 11.254 9104 Z= 0.308 Chirality : 0.045 0.149 964 Planarity : 0.003 0.039 1176 Dihedral : 4.272 20.072 955 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.85 % Allowed : 19.80 % Favored : 78.35 % 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: -0.90 (0.30), residues: 814 helix: -3.97 (0.77), residues: 20 sheet: 0.09 (0.31), residues: 272 loop : -0.84 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 50 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE A 400 TYR 0.015 0.001 TYR A 495 ARG 0.006 0.000 ARG F 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1777.00 seconds wall clock time: 32 minutes 9.21 seconds (1929.21 seconds total)