Starting phenix.real_space_refine on Thu Jun 5 16:33:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zc5_39923/06_2025/8zc5_39923.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zc5_39923/06_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_39923/06_2025/8zc5_39923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zc5_39923/06_2025/8zc5_39923.map" model { file = "/net/cci-nas-00/data/ceres_data/8zc5_39923/06_2025/8zc5_39923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zc5_39923/06_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-5710/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: 5.29, per 1000 atoms: 0.81 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: 1.52 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: 0.80 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: 1.89 Time building geometry restraints manager: 1.83 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: 1.540 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.460 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.470 ------------------------------------------------------------------------------- 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 6709 Z= 0.183 Angle : 0.764 10.951 9134 Z= 0.407 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00784 ( 2) link_NAG-ASN : angle 3.84938 ( 6) hydrogen bonds : bond 0.25938 ( 158) hydrogen bonds : angle 10.22660 ( 444) SS BOND : bond 0.00614 ( 12) SS BOND : angle 1.44136 ( 24) covalent geometry : bond 0.00383 ( 6695) covalent geometry : angle 0.75542 ( 9104) *********************** 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 : 0.744 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: 0.1976 time to fit residues: 43.2483 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 : 0.795 ------------------------------------------------------------------------------- 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: 0.9980 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 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 6709 Z= 0.172 Angle : 0.611 9.635 9134 Z= 0.317 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 2) link_NAG-ASN : angle 1.53537 ( 6) hydrogen bonds : bond 0.04071 ( 158) hydrogen bonds : angle 6.83862 ( 444) SS BOND : bond 0.00207 ( 12) SS BOND : angle 1.11465 ( 24) covalent geometry : bond 0.00402 ( 6695) covalent geometry : angle 0.60770 ( 9104) *********************** 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 : 0.741 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: 0.1966 time to fit residues: 37.0600 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 : 0.750 ------------------------------------------------------------------------------- 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: 0.0980 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: 0.7980 chunk 28 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- 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 = 0.168110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.137903 restraints weight = 8943.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.137036 restraints weight = 12606.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.138896 restraints weight = 11309.483| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6709 Z= 0.117 Angle : 0.568 7.806 9134 Z= 0.288 Chirality : 0.045 0.148 964 Planarity : 0.004 0.034 1176 Dihedral : 4.407 20.568 955 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.14 % Allowed : 13.68 % 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 (0.75), residues: 20 sheet: 0.13 (0.30), residues: 274 loop : -1.08 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 50 HIS 0.002 0.000 HIS E 35 PHE 0.016 0.001 PHE A 400 TYR 0.014 0.001 TYR A 495 ARG 0.006 0.000 ARG F 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00112 ( 2) link_NAG-ASN : angle 1.33244 ( 6) hydrogen bonds : bond 0.03312 ( 158) hydrogen bonds : angle 6.00985 ( 444) SS BOND : bond 0.00206 ( 12) SS BOND : angle 0.97913 ( 24) covalent geometry : bond 0.00273 ( 6695) covalent geometry : angle 0.56548 ( 9104) *********************** 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 148 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8244 (m-40) cc_final: 0.7859 (t0) REVERT: B 467 ASP cc_start: 0.8223 (p0) cc_final: 0.7847 (p0) REVERT: D 6 GLN cc_start: 0.8516 (pt0) cc_final: 0.7912 (pt0) REVERT: E 76 ILE cc_start: 0.8511 (pt) cc_final: 0.8142 (pt) REVERT: E 80 TYR cc_start: 0.8031 (m-10) cc_final: 0.7665 (m-10) REVERT: F 39 GLN cc_start: 0.7481 (tp40) cc_final: 0.7270 (tp40) REVERT: F 91 THR cc_start: 0.7984 (p) cc_final: 0.7696 (p) outliers start: 8 outliers final: 5 residues processed: 143 average time/residue: 0.2010 time to fit residues: 37.2397 Evaluate side-chains 138 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 133 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain E residue 124 THR 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: 0.9990 chunk 14 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 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: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.165420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.126227 restraints weight = 8996.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.128014 restraints weight = 7815.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.129127 restraints weight = 6487.011| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6709 Z= 0.161 Angle : 0.574 8.308 9134 Z= 0.293 Chirality : 0.045 0.148 964 Planarity : 0.004 0.037 1176 Dihedral : 4.390 16.871 955 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.42 % Allowed : 15.10 % Favored : 83.48 % 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: -1.08 (0.30), residues: 814 helix: -3.77 (0.77), residues: 20 sheet: -0.04 (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 0.017 0.001 TYR A 495 ARG 0.007 0.000 ARG D 80 Details of bonding type rmsd link_NAG-ASN : bond 0.00073 ( 2) link_NAG-ASN : angle 1.21917 ( 6) hydrogen bonds : bond 0.03218 ( 158) hydrogen bonds : angle 5.71443 ( 444) SS BOND : bond 0.00226 ( 12) SS BOND : angle 0.93786 ( 24) covalent geometry : bond 0.00379 ( 6695) covalent geometry : angle 0.57192 ( 9104) *********************** 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 146 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8312 (m-40) cc_final: 0.7854 (t0) REVERT: B 467 ASP cc_start: 0.8285 (p0) cc_final: 0.7931 (p0) REVERT: B 498 ARG cc_start: 0.8552 (mtt-85) cc_final: 0.7885 (mtt-85) REVERT: D 6 GLN cc_start: 0.8649 (pt0) cc_final: 0.8139 (pt0) REVERT: E 80 TYR cc_start: 0.8085 (m-10) cc_final: 0.7756 (m-10) REVERT: F 39 GLN cc_start: 0.7633 (tp40) cc_final: 0.7263 (tp40) REVERT: F 119 GLN cc_start: 0.8227 (mp10) cc_final: 0.7863 (mp10) outliers start: 10 outliers final: 8 residues processed: 143 average time/residue: 0.2076 time to fit residues: 38.2166 Evaluate side-chains 137 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 0.0670 chunk 70 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.158114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.121409 restraints weight = 9140.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.122050 restraints weight = 7811.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.122486 restraints weight = 7285.029| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 6709 Z= 0.353 Angle : 0.754 11.180 9134 Z= 0.387 Chirality : 0.050 0.182 964 Planarity : 0.005 0.055 1176 Dihedral : 5.236 20.029 955 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.14 % Allowed : 16.52 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.29), residues: 814 helix: -4.62 (0.49), residues: 28 sheet: -0.11 (0.30), residues: 269 loop : -1.15 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 50 HIS 0.004 0.001 HIS E 35 PHE 0.028 0.003 PHE B 400 TYR 0.037 0.002 TYR B 453 ARG 0.009 0.001 ARG C 26 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 2) link_NAG-ASN : angle 1.24893 ( 6) hydrogen bonds : bond 0.04217 ( 158) hydrogen bonds : angle 6.20920 ( 444) SS BOND : bond 0.00366 ( 12) SS BOND : angle 1.44913 ( 24) covalent geometry : bond 0.00835 ( 6695) covalent geometry : angle 0.75074 ( 9104) *********************** 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 142 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 467 ASP cc_start: 0.8437 (p0) cc_final: 0.7990 (p0) REVERT: B 498 ARG cc_start: 0.8773 (mtt-85) cc_final: 0.8138 (mtt-85) REVERT: D 6 GLN cc_start: 0.8779 (pt0) cc_final: 0.8276 (pt0) REVERT: F 67 ARG cc_start: 0.6847 (mtm-85) cc_final: 0.6209 (mtm-85) REVERT: F 81 MET cc_start: 0.7318 (tmm) cc_final: 0.7014 (tmm) REVERT: F 119 GLN cc_start: 0.8502 (mp10) cc_final: 0.8126 (mp10) outliers start: 15 outliers final: 11 residues processed: 136 average time/residue: 0.1963 time to fit residues: 35.3183 Evaluate side-chains 134 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 D residue 83 ASP 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: 0.9990 chunk 52 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 3 optimal weight: 0.0980 chunk 36 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.162365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.128050 restraints weight = 8877.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.128084 restraints weight = 8292.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.128084 restraints weight = 7622.565| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6709 Z= 0.160 Angle : 0.636 11.195 9134 Z= 0.318 Chirality : 0.046 0.149 964 Planarity : 0.004 0.038 1176 Dihedral : 4.835 18.491 955 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % 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: -1.30 (0.30), residues: 814 helix: -4.57 (0.51), residues: 26 sheet: -0.10 (0.30), residues: 269 loop : -1.10 (0.29), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 111 HIS 0.003 0.001 HIS E 35 PHE 0.018 0.002 PHE A 400 TYR 0.020 0.001 TYR B 453 ARG 0.007 0.000 ARG D 80 Details of bonding type rmsd link_NAG-ASN : bond 0.00040 ( 2) link_NAG-ASN : angle 1.25540 ( 6) hydrogen bonds : bond 0.03236 ( 158) hydrogen bonds : angle 5.71096 ( 444) SS BOND : bond 0.00330 ( 12) SS BOND : angle 1.27197 ( 24) covalent geometry : bond 0.00376 ( 6695) covalent geometry : angle 0.63278 ( 9104) *********************** 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 143 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 467 ASP cc_start: 0.8402 (p0) cc_final: 0.7948 (p0) REVERT: B 498 ARG cc_start: 0.8679 (mtt-85) cc_final: 0.8119 (mtt-85) REVERT: C 26 ARG cc_start: 0.8197 (mtp-110) cc_final: 0.7652 (mtp85) REVERT: D 6 GLN cc_start: 0.8784 (pt0) cc_final: 0.8219 (pt0) REVERT: E 70 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8471 (ttp) REVERT: F 67 ARG cc_start: 0.6836 (mtm-85) cc_final: 0.6535 (mtm-85) REVERT: F 119 GLN cc_start: 0.8434 (mp10) cc_final: 0.8083 (mp10) outliers start: 11 outliers final: 9 residues processed: 138 average time/residue: 0.1927 time to fit residues: 34.9629 Evaluate side-chains 137 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 385 THR 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 Chi-restraints excluded: chain E residue 125 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 27 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 19 optimal weight: 0.0070 chunk 71 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 50 optimal weight: 0.0070 chunk 31 optimal weight: 3.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.161071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.140490 restraints weight = 8850.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.137618 restraints weight = 16872.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.138327 restraints weight = 16811.289| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6709 Z= 0.134 Angle : 0.607 10.905 9134 Z= 0.304 Chirality : 0.046 0.144 964 Planarity : 0.003 0.038 1176 Dihedral : 4.538 17.161 955 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.71 % Allowed : 19.37 % 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: -1.19 (0.30), residues: 814 helix: -4.58 (0.45), residues: 26 sheet: -0.00 (0.30), residues: 268 loop : -1.03 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 50 HIS 0.003 0.001 HIS E 35 PHE 0.016 0.001 PHE A 400 TYR 0.016 0.001 TYR B 453 ARG 0.006 0.000 ARG D 80 Details of bonding type rmsd link_NAG-ASN : bond 0.00057 ( 2) link_NAG-ASN : angle 1.20306 ( 6) hydrogen bonds : bond 0.02981 ( 158) hydrogen bonds : angle 5.48224 ( 444) SS BOND : bond 0.00358 ( 12) SS BOND : angle 1.16632 ( 24) covalent geometry : bond 0.00318 ( 6695) covalent geometry : angle 0.60409 ( 9104) *********************** 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 141 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 467 ASP cc_start: 0.8260 (p0) cc_final: 0.7921 (p0) REVERT: B 498 ARG cc_start: 0.8295 (mtt-85) cc_final: 0.7882 (mtt-85) REVERT: D 6 GLN cc_start: 0.8711 (pt0) cc_final: 0.8134 (pt0) outliers start: 12 outliers final: 9 residues processed: 138 average time/residue: 0.1954 time to fit residues: 35.1245 Evaluate side-chains 132 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 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 125 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 52 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.3803 r_free = 0.3803 target = 0.160192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.121725 restraints weight = 8972.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.123091 restraints weight = 7606.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.123655 restraints weight = 6485.303| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 6709 Z= 0.255 Angle : 0.693 12.388 9134 Z= 0.349 Chirality : 0.047 0.161 964 Planarity : 0.004 0.039 1176 Dihedral : 4.878 18.330 955 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.14 % Allowed : 19.66 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.30), residues: 814 helix: -4.61 (0.49), residues: 26 sheet: -0.21 (0.30), residues: 279 loop : -1.02 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 50 HIS 0.005 0.001 HIS E 35 PHE 0.023 0.002 PHE A 429 TYR 0.025 0.002 TYR B 453 ARG 0.005 0.000 ARG F 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00141 ( 2) link_NAG-ASN : angle 1.20956 ( 6) hydrogen bonds : bond 0.03546 ( 158) hydrogen bonds : angle 5.76701 ( 444) SS BOND : bond 0.00456 ( 12) SS BOND : angle 1.42389 ( 24) covalent geometry : bond 0.00604 ( 6695) covalent geometry : angle 0.68963 ( 9104) *********************** 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 140 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 467 ASP cc_start: 0.8372 (p0) cc_final: 0.7927 (p0) REVERT: B 493 GLN cc_start: 0.8227 (tp-100) cc_final: 0.8016 (tm-30) REVERT: C 26 ARG cc_start: 0.8083 (mtp-110) cc_final: 0.7663 (mtp85) REVERT: C 29 ILE cc_start: 0.8355 (mm) cc_final: 0.8149 (mm) REVERT: D 6 GLN cc_start: 0.8873 (pt0) cc_final: 0.8321 (pt0) REVERT: D 38 GLN cc_start: 0.8800 (mt0) cc_final: 0.8488 (mp10) REVERT: F 81 MET cc_start: 0.7308 (tmm) cc_final: 0.6979 (tmm) outliers start: 15 outliers final: 13 residues processed: 135 average time/residue: 0.1913 time to fit residues: 34.1120 Evaluate side-chains 137 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 385 THR Chi-restraints excluded: chain B residue 425 LEU 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 11 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 125 VAL 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: 1.9990 chunk 24 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 71 optimal weight: 0.8980 chunk 45 optimal weight: 0.0980 chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3795 r_free = 0.3795 target = 0.160613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.143992 restraints weight = 8944.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.142443 restraints weight = 15295.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.142383 restraints weight = 16327.587| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6709 Z= 0.142 Angle : 0.632 11.922 9134 Z= 0.317 Chirality : 0.046 0.151 964 Planarity : 0.003 0.038 1176 Dihedral : 4.585 17.421 955 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.71 % Allowed : 20.80 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.30), residues: 814 helix: -4.59 (0.44), residues: 26 sheet: -0.04 (0.30), residues: 268 loop : -1.03 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 111 HIS 0.003 0.001 HIS E 35 PHE 0.023 0.001 PHE A 429 TYR 0.029 0.001 TYR A 495 ARG 0.006 0.000 ARG F 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00055 ( 2) link_NAG-ASN : angle 1.21125 ( 6) hydrogen bonds : bond 0.02971 ( 158) hydrogen bonds : angle 5.48279 ( 444) SS BOND : bond 0.00326 ( 12) SS BOND : angle 1.18529 ( 24) covalent geometry : bond 0.00340 ( 6695) covalent geometry : angle 0.62956 ( 9104) *********************** 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 145 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 386 LYS cc_start: 0.5175 (pttt) cc_final: 0.3974 (tttt) REVERT: B 467 ASP cc_start: 0.8239 (p0) cc_final: 0.7874 (p0) REVERT: D 6 GLN cc_start: 0.8666 (pt0) cc_final: 0.8139 (pt0) REVERT: F 122 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6060 (pt) outliers start: 12 outliers final: 11 residues processed: 142 average time/residue: 0.1920 time to fit residues: 35.6817 Evaluate side-chains 140 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 385 THR 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 11 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 125 VAL 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: 2.9990 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 75 optimal weight: 0.0970 chunk 40 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- 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 = 0.3828 r_free = 0.3828 target = 0.162423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.125863 restraints weight = 8966.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.126789 restraints weight = 7800.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.127072 restraints weight = 6593.931| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6709 Z= 0.182 Angle : 0.674 13.017 9134 Z= 0.338 Chirality : 0.046 0.155 964 Planarity : 0.004 0.039 1176 Dihedral : 4.630 17.562 955 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.71 % Allowed : 21.65 % Favored : 76.64 % 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: -1.25 (0.30), residues: 814 helix: -4.60 (0.45), residues: 26 sheet: -0.07 (0.30), residues: 268 loop : -1.06 (0.29), residues: 520 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 0.024 0.002 PHE A 429 TYR 0.030 0.002 TYR A 495 ARG 0.009 0.001 ARG B 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00040 ( 2) link_NAG-ASN : angle 1.14241 ( 6) hydrogen bonds : bond 0.03070 ( 158) hydrogen bonds : angle 5.51868 ( 444) SS BOND : bond 0.00359 ( 12) SS BOND : angle 1.28642 ( 24) covalent geometry : bond 0.00437 ( 6695) covalent geometry : angle 0.67132 ( 9104) ********************** 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 143 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 386 LYS cc_start: 0.4854 (pttt) cc_final: 0.3926 (tttt) REVERT: B 467 ASP cc_start: 0.8297 (p0) cc_final: 0.7898 (p0) REVERT: D 6 GLN cc_start: 0.8849 (pt0) cc_final: 0.8269 (pt0) REVERT: D 80 ARG cc_start: 0.5884 (mmp80) cc_final: 0.5653 (mmp80) REVERT: F 81 MET cc_start: 0.7209 (tmm) cc_final: 0.6962 (tmm) outliers start: 12 outliers final: 11 residues processed: 141 average time/residue: 0.2022 time to fit residues: 37.2569 Evaluate side-chains 136 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 385 THR 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 11 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 125 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 29 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 8 optimal weight: 0.2980 chunk 77 optimal weight: 0.1980 chunk 30 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.163541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.127930 restraints weight = 9094.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.129054 restraints weight = 7987.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.129548 restraints weight = 7169.783| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6709 Z= 0.152 Angle : 0.662 13.004 9134 Z= 0.331 Chirality : 0.046 0.153 964 Planarity : 0.004 0.040 1176 Dihedral : 4.565 21.029 955 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.85 % Allowed : 21.51 % Favored : 76.64 % 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: -1.25 (0.30), residues: 814 helix: -4.60 (0.42), residues: 26 sheet: -0.16 (0.30), residues: 272 loop : -1.00 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 50 HIS 0.004 0.001 HIS E 35 PHE 0.024 0.002 PHE A 429 TYR 0.028 0.001 TYR A 495 ARG 0.009 0.000 ARG B 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00055 ( 2) link_NAG-ASN : angle 1.13204 ( 6) hydrogen bonds : bond 0.02880 ( 158) hydrogen bonds : angle 5.47586 ( 444) SS BOND : bond 0.00349 ( 12) SS BOND : angle 1.13039 ( 24) covalent geometry : bond 0.00364 ( 6695) covalent geometry : angle 0.65959 ( 9104) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2549.38 seconds wall clock time: 44 minutes 50.28 seconds (2690.28 seconds total)