Starting phenix.real_space_refine on Tue Mar 11 18:16:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zc5_39923/03_2025/8zc5_39923.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zc5_39923/03_2025/8zc5_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/cci-nas-00/data/ceres_data/8zc5_39923/03_2025/8zc5_39923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zc5_39923/03_2025/8zc5_39923.map" model { file = "/net/cci-nas-00/data/ceres_data/8zc5_39923/03_2025/8zc5_39923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zc5_39923/03_2025/8zc5_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. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.48, per 1000 atoms: 0.69 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 - 3.00 Amino acid : True - 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: 1.32 Conformation dependent library (CDL) restraints added in 853.6 milliseconds 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: 0.95 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: 1.85 Time building geometry restraints manager: 1.62 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: 0.00 - 2.19: 8884 2.19 - 4.38: 185 4.38 - 6.57: 29 6.57 - 8.76: 5 8.76 - 10.95: 1 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: 1.270 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.470 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.980 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.747 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: 0.1965 time to fit residues: 43.1037 Evaluate side-chains 136 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.167152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.136821 restraints weight = 8784.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.134923 restraints weight = 11993.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.136732 restraints weight = 10847.232| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 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 9.635 9104 Z= 0.316 Chirality : 0.047 0.156 964 Planarity : 0.004 0.035 1176 Dihedral : 4.729 25.061 955 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 to be fit. rotamer outliers: 4 poor density : 142 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: B 467 ASP cc_start: 0.8239 (p0) cc_final: 0.7877 (p0) REVERT: C 47 LEU cc_start: 0.8091 (tp) cc_final: 0.7830 (tp) REVERT: D 6 GLN cc_start: 0.8562 (pt0) cc_final: 0.7719 (pt0) REVERT: F 39 GLN cc_start: 0.7737 (tp40) cc_final: 0.7516 (tp40) outliers start: 4 outliers final: 3 residues processed: 144 average time/residue: 0.2030 time to fit residues: 38.4016 Evaluate side-chains 138 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 135 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 48 optimal weight: 0.8980 chunk 61 optimal weight: 0.0770 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 0.0470 chunk 29 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 40 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 28 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.2236 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.169312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.138930 restraints weight = 8921.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.136976 restraints weight = 11712.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.139169 restraints weight = 10804.950| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6695 Z= 0.158 Angle : 0.560 7.555 9104 Z= 0.284 Chirality : 0.045 0.150 964 Planarity : 0.004 0.034 1176 Dihedral : 4.378 20.986 955 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.85 % Allowed : 13.96 % Favored : 85.19 % 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: -1.07 (0.29), residues: 814 helix: -3.80 (0.74), residues: 20 sheet: 0.16 (0.30), residues: 274 loop : -1.09 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 50 HIS 0.002 0.000 HIS E 35 PHE 0.015 0.001 PHE A 400 TYR 0.013 0.001 TYR B 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 147 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8218 (m-40) cc_final: 0.7835 (t0) REVERT: B 467 ASP cc_start: 0.8212 (p0) cc_final: 0.7850 (p0) REVERT: C 47 LEU cc_start: 0.7991 (tp) cc_final: 0.7694 (tp) REVERT: D 6 GLN cc_start: 0.8502 (pt0) cc_final: 0.7883 (pt0) REVERT: F 39 GLN cc_start: 0.7558 (tp40) cc_final: 0.7281 (tp40) REVERT: F 91 THR cc_start: 0.7970 (p) cc_final: 0.7677 (p) outliers start: 6 outliers final: 2 residues processed: 144 average time/residue: 0.2105 time to fit residues: 39.5740 Evaluate side-chains 137 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 52 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 60 optimal weight: 0.0030 chunk 14 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.8192 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.165179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.125944 restraints weight = 9014.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.127486 restraints weight = 7598.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.128337 restraints weight = 6666.176| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1931 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= 0.288 Angle : 0.588 8.537 9104 Z= 0.300 Chirality : 0.046 0.149 964 Planarity : 0.004 0.037 1176 Dihedral : 4.448 17.104 955 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.28 % Allowed : 14.81 % Favored : 83.90 % 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: -1.10 (0.30), residues: 814 helix: -3.83 (0.76), residues: 20 sheet: -0.04 (0.30), residues: 282 loop : -1.01 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 50 HIS 0.004 0.001 HIS E 35 PHE 0.017 0.002 PHE A 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 142 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8206 (m-40) cc_final: 0.7858 (t0) REVERT: B 467 ASP cc_start: 0.8292 (p0) cc_final: 0.7943 (p0) REVERT: B 498 ARG cc_start: 0.8573 (mtt-85) cc_final: 0.7911 (mtt-85) REVERT: D 6 GLN cc_start: 0.8662 (pt0) cc_final: 0.8052 (pt0) REVERT: F 39 GLN cc_start: 0.7628 (tp40) cc_final: 0.7279 (tp40) REVERT: F 81 MET cc_start: 0.7150 (tmm) cc_final: 0.6850 (tmm) REVERT: F 119 GLN cc_start: 0.8171 (mp10) cc_final: 0.7819 (mp10) outliers start: 9 outliers final: 7 residues processed: 140 average time/residue: 0.2093 time to fit residues: 38.0346 Evaluate side-chains 133 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 8 optimal weight: 0.0970 chunk 41 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 0.0980 chunk 70 optimal weight: 0.6980 chunk 72 optimal weight: 0.1980 chunk 46 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 0.1980 chunk 69 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.2578 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.168326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.139042 restraints weight = 8954.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.136409 restraints weight = 11989.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.138389 restraints weight = 10942.643| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6695 Z= 0.158 Angle : 0.545 9.205 9104 Z= 0.276 Chirality : 0.045 0.143 964 Planarity : 0.003 0.037 1176 Dihedral : 4.205 17.249 955 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.00 % Allowed : 16.95 % Favored : 82.05 % 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: -1.02 (0.30), residues: 814 helix: -4.04 (0.61), residues: 26 sheet: 0.23 (0.30), residues: 270 loop : -1.02 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 50 HIS 0.002 0.000 HIS E 35 PHE 0.020 0.001 PHE A 429 TYR 0.013 0.001 TYR B 495 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 153 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8232 (m-40) cc_final: 0.7870 (t0) REVERT: B 467 ASP cc_start: 0.8229 (p0) cc_final: 0.7883 (p0) REVERT: B 498 ARG cc_start: 0.8462 (mtt-85) cc_final: 0.7815 (mtt-85) REVERT: D 6 GLN cc_start: 0.8573 (pt0) cc_final: 0.8069 (pt0) REVERT: E 50 TRP cc_start: 0.9021 (p90) cc_final: 0.8519 (p90) REVERT: F 91 THR cc_start: 0.8000 (p) cc_final: 0.7713 (p) REVERT: F 119 GLN cc_start: 0.8244 (mp10) cc_final: 0.7926 (mp10) outliers start: 7 outliers final: 6 residues processed: 149 average time/residue: 0.2209 time to fit residues: 42.2794 Evaluate side-chains 142 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 136 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 74 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 46 optimal weight: 0.0570 chunk 52 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.166703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.128453 restraints weight = 8901.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.129942 restraints weight = 7724.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.130805 restraints weight = 6365.016| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6695 Z= 0.224 Angle : 0.575 10.644 9104 Z= 0.287 Chirality : 0.045 0.153 964 Planarity : 0.004 0.049 1176 Dihedral : 4.193 15.936 955 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.57 % Allowed : 16.95 % Favored : 81.48 % 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: -4.05 (0.62), residues: 26 sheet: 0.08 (0.30), residues: 274 loop : -0.98 (0.29), residues: 514 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 0.021 0.001 PHE A 429 TYR 0.014 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 150 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.778 Fit side-chains REVERT: A 405 ASN cc_start: 0.8269 (m-40) cc_final: 0.7832 (t0) REVERT: A 472 ILE cc_start: 0.9162 (tp) cc_final: 0.8914 (tt) REVERT: B 386 LYS cc_start: 0.5169 (pttt) cc_final: 0.3823 (tttt) REVERT: B 467 ASP cc_start: 0.8276 (p0) cc_final: 0.7951 (p0) REVERT: C 26 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7433 (mtp85) REVERT: D 6 GLN cc_start: 0.8684 (pt0) cc_final: 0.8139 (pt0) REVERT: D 74 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7685 (tt) REVERT: E 50 TRP cc_start: 0.9177 (p90) cc_final: 0.8691 (p90) REVERT: E 80 TYR cc_start: 0.8022 (m-10) cc_final: 0.7676 (m-10) REVERT: F 81 MET cc_start: 0.7075 (tmm) cc_final: 0.6789 (tmm) REVERT: F 91 THR cc_start: 0.8155 (p) cc_final: 0.7886 (p) REVERT: F 119 GLN cc_start: 0.8377 (mp10) cc_final: 0.7977 (mp10) REVERT: F 122 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.6422 (pp) outliers start: 11 outliers final: 6 residues processed: 144 average time/residue: 0.2378 time to fit residues: 43.7557 Evaluate side-chains 142 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 122 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 27 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.164850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.126285 restraints weight = 8904.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.127288 restraints weight = 7266.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.127660 restraints weight = 6376.587| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2226 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= 0.286 Angle : 0.623 11.485 9104 Z= 0.310 Chirality : 0.046 0.146 964 Planarity : 0.004 0.044 1176 Dihedral : 4.354 16.081 955 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.14 % Allowed : 17.95 % Favored : 79.91 % 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: -0.99 (0.30), residues: 814 helix: -3.89 (0.74), residues: 20 sheet: -0.05 (0.30), residues: 282 loop : -0.88 (0.29), residues: 512 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 0.021 0.002 PHE A 429 TYR 0.017 0.002 TYR A 495 ARG 0.010 0.000 ARG C 26 *********************** 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 151 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.687 Fit side-chains REVERT: A 429 PHE cc_start: 0.7570 (t80) cc_final: 0.7233 (t80) REVERT: B 386 LYS cc_start: 0.5109 (pttt) cc_final: 0.3984 (tttt) REVERT: B 467 ASP cc_start: 0.8314 (p0) cc_final: 0.7959 (p0) REVERT: D 6 GLN cc_start: 0.8718 (pt0) cc_final: 0.8181 (pt0) REVERT: D 74 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7690 (tt) REVERT: F 81 MET cc_start: 0.7132 (tmm) cc_final: 0.6839 (tmm) REVERT: F 91 THR cc_start: 0.8170 (p) cc_final: 0.7914 (p) REVERT: F 112 MET cc_start: 0.8266 (tpp) cc_final: 0.7978 (tpp) REVERT: F 119 GLN cc_start: 0.8398 (mp10) cc_final: 0.8029 (mp10) REVERT: F 122 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.6013 (pp) outliers start: 15 outliers final: 10 residues processed: 144 average time/residue: 0.2045 time to fit residues: 38.2479 Evaluate side-chains 144 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 122 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 21 optimal weight: 0.3980 chunk 52 optimal weight: 10.0000 chunk 32 optimal weight: 0.0040 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.165587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.128224 restraints weight = 8862.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.129347 restraints weight = 7623.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.130013 restraints weight = 6822.930| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2340 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= 0.235 Angle : 0.620 11.452 9104 Z= 0.306 Chirality : 0.046 0.156 964 Planarity : 0.004 0.043 1176 Dihedral : 4.376 19.487 955 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.71 % Allowed : 18.52 % Favored : 79.77 % 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: -1.02 (0.30), residues: 814 helix: -3.97 (0.72), residues: 20 sheet: 0.03 (0.30), residues: 272 loop : -0.94 (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 0.020 0.001 PHE A 429 TYR 0.016 0.001 TYR B 453 ARG 0.010 0.001 ARG C 26 *********************** 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 154 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.896 Fit side-chains REVERT: B 386 LYS cc_start: 0.4864 (pttt) cc_final: 0.3891 (tttt) REVERT: B 467 ASP cc_start: 0.8284 (p0) cc_final: 0.7941 (p0) REVERT: D 6 GLN cc_start: 0.8721 (pt0) cc_final: 0.8192 (pt0) REVERT: E 80 TYR cc_start: 0.8055 (m-10) cc_final: 0.7726 (m-10) REVERT: F 91 THR cc_start: 0.8181 (p) cc_final: 0.7919 (p) REVERT: F 112 MET cc_start: 0.8148 (tpp) cc_final: 0.7935 (tpp) REVERT: F 119 GLN cc_start: 0.8352 (mp10) cc_final: 0.8033 (mp10) REVERT: F 122 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.5980 (pp) outliers start: 12 outliers final: 9 residues processed: 148 average time/residue: 0.2037 time to fit residues: 39.2710 Evaluate side-chains 142 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 511 VAL 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 Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 122 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 38 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 45 optimal weight: 0.0070 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 54 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.165498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.136341 restraints weight = 8923.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.135236 restraints weight = 13039.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.137197 restraints weight = 12221.677| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2399 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= 0.235 Angle : 0.634 11.551 9104 Z= 0.312 Chirality : 0.046 0.159 964 Planarity : 0.004 0.039 1176 Dihedral : 4.395 19.190 955 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.14 % Allowed : 18.95 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.30), residues: 814 helix: -4.05 (0.72), residues: 20 sheet: 0.03 (0.30), residues: 272 loop : -0.97 (0.28), 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 0.023 0.001 PHE A 429 TYR 0.017 0.001 TYR B 489 ARG 0.007 0.001 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 to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.655 Fit side-chains REVERT: B 386 LYS cc_start: 0.4997 (pttt) cc_final: 0.3878 (tttt) REVERT: B 467 ASP cc_start: 0.8273 (p0) cc_final: 0.7905 (p0) REVERT: D 6 GLN cc_start: 0.8667 (pt0) cc_final: 0.8143 (pt0) REVERT: E 80 TYR cc_start: 0.8041 (m-10) cc_final: 0.7760 (m-10) REVERT: F 112 MET cc_start: 0.8018 (tpp) cc_final: 0.7798 (tpp) REVERT: F 119 GLN cc_start: 0.8254 (mp10) cc_final: 0.8014 (mp10) REVERT: F 122 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6226 (tp) outliers start: 15 outliers final: 11 residues processed: 143 average time/residue: 0.2123 time to fit residues: 39.2589 Evaluate side-chains 143 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 433 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain B residue 349 SER 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 Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 122 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 73 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 55 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 54 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.164593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.135663 restraints weight = 8922.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.134500 restraints weight = 12821.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.136464 restraints weight = 12026.200| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6695 Z= 0.251 Angle : 0.632 11.861 9104 Z= 0.316 Chirality : 0.046 0.153 964 Planarity : 0.004 0.039 1176 Dihedral : 4.405 20.145 955 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.14 % Allowed : 18.66 % Favored : 79.20 % 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: -1.22 (0.29), residues: 814 helix: -4.41 (0.48), residues: 32 sheet: 0.02 (0.30), residues: 272 loop : -1.04 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 50 HIS 0.004 0.001 HIS E 35 PHE 0.024 0.001 PHE A 429 TYR 0.018 0.001 TYR B 489 ARG 0.007 0.000 ARG F 67 ********************** 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 148 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.738 Fit side-chains REVERT: B 386 LYS cc_start: 0.4767 (pttt) cc_final: 0.3874 (tttt) REVERT: B 467 ASP cc_start: 0.8287 (p0) cc_final: 0.7912 (p0) REVERT: D 6 GLN cc_start: 0.8713 (pt0) cc_final: 0.8178 (pt0) REVERT: E 80 TYR cc_start: 0.8078 (m-10) cc_final: 0.7800 (m-10) REVERT: F 112 MET cc_start: 0.8016 (tpp) cc_final: 0.7812 (tpp) REVERT: F 119 GLN cc_start: 0.8268 (mp10) cc_final: 0.8062 (mp10) REVERT: F 122 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6399 (tp) outliers start: 15 outliers final: 14 residues processed: 141 average time/residue: 0.2125 time to fit residues: 38.9592 Evaluate side-chains 146 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 433 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain B residue 349 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 81 MET Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 122 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 29 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 54 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.164297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.125418 restraints weight = 9078.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.127124 restraints weight = 7565.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.128567 restraints weight = 6405.060| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6695 Z= 0.256 Angle : 0.638 12.220 9104 Z= 0.318 Chirality : 0.046 0.150 964 Planarity : 0.004 0.039 1176 Dihedral : 4.419 19.739 955 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.99 % Allowed : 19.23 % Favored : 78.77 % 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: -1.23 (0.29), residues: 814 helix: -4.41 (0.48), residues: 32 sheet: -0.01 (0.30), residues: 272 loop : -1.04 (0.29), residues: 510 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 0.024 0.001 PHE A 429 TYR 0.021 0.001 TYR B 489 ARG 0.007 0.000 ARG F 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2488.99 seconds wall clock time: 43 minutes 42.40 seconds (2622.40 seconds total)