Starting phenix.real_space_refine on Wed Sep 17 07:02:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zc5_39923/09_2025/8zc5_39923.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zc5_39923/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zc5_39923/09_2025/8zc5_39923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zc5_39923/09_2025/8zc5_39923.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zc5_39923/09_2025/8zc5_39923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zc5_39923/09_2025/8zc5_39923.map" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.81, per 1000 atoms: 0.28 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: 0.49 Conformation dependent library (CDL) restraints added in 343.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.32 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: 0.92 Time building geometry restraints manager: 0.69 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: 1.790 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.700 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.020 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.015 0.001 ARG F 67 TYR 0.030 0.002 TYR A 495 PHE 0.037 0.002 PHE A 456 TRP 0.029 0.002 TRP E 50 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 6695) covalent geometry : angle 0.75542 ( 9104) SS BOND : bond 0.00614 ( 12) SS BOND : angle 1.44136 ( 24) hydrogen bonds : bond 0.25938 ( 158) hydrogen bonds : angle 10.22660 ( 444) link_NAG-ASN : bond 0.00784 ( 2) link_NAG-ASN : angle 3.84938 ( 6) *********************** 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 : 0.218 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: 0.0868 time to fit residues: 19.0640 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 : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.165252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.127746 restraints weight = 8960.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.129157 restraints weight = 7352.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.129695 restraints weight = 6213.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.130730 restraints weight = 5618.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.130836 restraints weight = 5596.059| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6709 Z= 0.208 Angle : 0.630 9.769 9134 Z= 0.327 Chirality : 0.047 0.152 964 Planarity : 0.004 0.035 1176 Dihedral : 4.820 24.145 955 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.71 % Allowed : 12.11 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.29), residues: 814 helix: -3.72 (0.80), residues: 20 sheet: -0.14 (0.30), residues: 279 loop : -1.12 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 80 TYR 0.019 0.001 TYR A 495 PHE 0.028 0.002 PHE F 29 TRP 0.018 0.002 TRP F 36 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 6695) covalent geometry : angle 0.62667 ( 9104) SS BOND : bond 0.00212 ( 12) SS BOND : angle 1.21399 ( 24) hydrogen bonds : bond 0.04299 ( 158) hydrogen bonds : angle 6.75459 ( 444) link_NAG-ASN : bond 0.00255 ( 2) link_NAG-ASN : angle 1.32343 ( 6) *********************** 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 148 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 143 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: B 467 ASP cc_start: 0.8273 (p0) cc_final: 0.7915 (p0) REVERT: C 47 LEU cc_start: 0.8164 (tp) cc_final: 0.7911 (tp) REVERT: D 6 GLN cc_start: 0.8630 (pt0) cc_final: 0.7774 (pt0) REVERT: F 81 MET cc_start: 0.7245 (tmm) cc_final: 0.7040 (tmm) outliers start: 5 outliers final: 3 residues processed: 145 average time/residue: 0.0877 time to fit residues: 16.5366 Evaluate side-chains 139 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 136 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain E residue 83 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 41 optimal weight: 3.9990 chunk 35 optimal weight: 0.0970 chunk 29 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 74 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.165213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.127520 restraints weight = 8880.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.128687 restraints weight = 7563.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.129216 restraints weight = 6605.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.129842 restraints weight = 5810.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.130038 restraints weight = 5867.747| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1724 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 : 0.593 8.528 9134 Z= 0.302 Chirality : 0.046 0.148 964 Planarity : 0.004 0.034 1176 Dihedral : 4.613 19.805 955 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.85 % Allowed : 13.82 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.29), residues: 814 helix: -3.78 (0.79), residues: 20 sheet: -0.01 (0.30), residues: 274 loop : -1.08 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 67 TYR 0.018 0.001 TYR A 495 PHE 0.019 0.001 PHE A 400 TRP 0.013 0.001 TRP E 50 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 6695) covalent geometry : angle 0.59046 ( 9104) SS BOND : bond 0.00384 ( 12) SS BOND : angle 1.01249 ( 24) hydrogen bonds : bond 0.03567 ( 158) hydrogen bonds : angle 6.12210 ( 444) link_NAG-ASN : bond 0.00069 ( 2) link_NAG-ASN : angle 1.26884 ( 6) *********************** 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 145 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: B 467 ASP cc_start: 0.8280 (p0) cc_final: 0.7914 (p0) REVERT: B 498 ARG cc_start: 0.8592 (mtt-85) cc_final: 0.8176 (mtt-85) REVERT: C 26 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7025 (ttp80) REVERT: D 6 GLN cc_start: 0.8650 (pt0) cc_final: 0.8001 (pt0) REVERT: E 80 TYR cc_start: 0.8133 (m-10) cc_final: 0.7848 (m-10) REVERT: E 105 LEU cc_start: 0.7984 (mt) cc_final: 0.7741 (mt) REVERT: F 39 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7327 (tp40) outliers start: 13 outliers final: 9 residues processed: 138 average time/residue: 0.0785 time to fit residues: 14.1590 Evaluate side-chains 142 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 511 VAL Chi-restraints excluded: chain C residue 26 ARG 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 Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 93 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 5 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.163287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.125795 restraints weight = 8945.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.127046 restraints weight = 7423.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.127293 restraints weight = 6432.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.127314 restraints weight = 6017.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.127477 restraints weight = 6072.003| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6709 Z= 0.191 Angle : 0.599 8.352 9134 Z= 0.306 Chirality : 0.046 0.151 964 Planarity : 0.004 0.036 1176 Dihedral : 4.602 16.639 955 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.99 % Allowed : 16.10 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.30), residues: 814 helix: -3.92 (0.73), residues: 20 sheet: -0.10 (0.30), residues: 278 loop : -1.05 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 80 TYR 0.019 0.001 TYR A 495 PHE 0.021 0.002 PHE B 400 TRP 0.013 0.001 TRP E 50 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 6695) covalent geometry : angle 0.59646 ( 9104) SS BOND : bond 0.00316 ( 12) SS BOND : angle 1.15691 ( 24) hydrogen bonds : bond 0.03415 ( 158) hydrogen bonds : angle 5.81816 ( 444) link_NAG-ASN : bond 0.00068 ( 2) link_NAG-ASN : angle 1.19516 ( 6) *********************** 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 152 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: B 467 ASP cc_start: 0.8309 (p0) cc_final: 0.7923 (p0) REVERT: C 26 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7110 (ttp80) REVERT: D 6 GLN cc_start: 0.8725 (pt0) cc_final: 0.8052 (pt0) REVERT: E 80 TYR cc_start: 0.8191 (m-10) cc_final: 0.7951 (m-10) REVERT: F 4 LEU cc_start: 0.8279 (tp) cc_final: 0.7920 (tp) REVERT: F 39 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7096 (tp40) REVERT: F 119 GLN cc_start: 0.8068 (mp10) cc_final: 0.7862 (mp10) outliers start: 14 outliers final: 9 residues processed: 145 average time/residue: 0.0889 time to fit residues: 16.6320 Evaluate side-chains 137 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 26 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 93 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 17 optimal weight: 0.0270 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.164962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.126370 restraints weight = 9028.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.128342 restraints weight = 7835.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.129110 restraints weight = 6413.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.130151 restraints weight = 5652.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.130239 restraints weight = 5663.694| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2067 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= 0.130 Angle : 0.568 7.795 9134 Z= 0.290 Chirality : 0.045 0.147 964 Planarity : 0.003 0.037 1176 Dihedral : 4.409 17.321 955 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.14 % Allowed : 17.38 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.30), residues: 814 helix: -3.88 (0.73), residues: 20 sheet: 0.05 (0.30), residues: 268 loop : -1.03 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 67 TYR 0.016 0.001 TYR B 453 PHE 0.016 0.001 PHE A 400 TRP 0.009 0.001 TRP E 36 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 6695) covalent geometry : angle 0.56639 ( 9104) SS BOND : bond 0.00228 ( 12) SS BOND : angle 0.90503 ( 24) hydrogen bonds : bond 0.03031 ( 158) hydrogen bonds : angle 5.57113 ( 444) link_NAG-ASN : bond 0.00067 ( 2) link_NAG-ASN : angle 1.22641 ( 6) *********************** 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 149 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: B 467 ASP cc_start: 0.8266 (p0) cc_final: 0.7923 (p0) REVERT: B 498 ARG cc_start: 0.8610 (mtt-85) cc_final: 0.8130 (mtt-85) REVERT: C 26 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6900 (ttp80) REVERT: D 6 GLN cc_start: 0.8721 (pt0) cc_final: 0.8128 (pt0) REVERT: E 80 TYR cc_start: 0.8208 (m-10) cc_final: 0.7883 (m-10) REVERT: F 4 LEU cc_start: 0.8384 (tp) cc_final: 0.8071 (tp) REVERT: F 39 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.7059 (tp40) outliers start: 15 outliers final: 10 residues processed: 144 average time/residue: 0.0948 time to fit residues: 17.6053 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 : 0.263 ------------------------------------------------------------------------------- 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 407 VAL Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 39 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 50 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 22 optimal weight: 0.0470 chunk 39 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 chunk 63 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 overall best weight: 0.4478 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.165285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.136357 restraints weight = 8930.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.135240 restraints weight = 13504.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.137248 restraints weight = 12412.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.137317 restraints weight = 8345.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.137903 restraints weight = 9234.120| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6709 Z= 0.127 Angle : 0.585 7.912 9134 Z= 0.293 Chirality : 0.045 0.145 964 Planarity : 0.003 0.038 1176 Dihedral : 4.353 18.475 955 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.42 % Allowed : 17.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.30), residues: 814 helix: -4.15 (0.59), residues: 26 sheet: 0.03 (0.30), residues: 268 loop : -1.05 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 67 TYR 0.015 0.001 TYR B 453 PHE 0.015 0.001 PHE A 400 TRP 0.009 0.001 TRP E 50 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6695) covalent geometry : angle 0.58204 ( 9104) SS BOND : bond 0.00298 ( 12) SS BOND : angle 1.07580 ( 24) hydrogen bonds : bond 0.02900 ( 158) hydrogen bonds : angle 5.40356 ( 444) link_NAG-ASN : bond 0.00074 ( 2) link_NAG-ASN : angle 1.20395 ( 6) *********************** 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: 17 poor density : 133 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 429 PHE cc_start: 0.7586 (t80) cc_final: 0.7368 (t80) REVERT: B 467 ASP cc_start: 0.8272 (p0) cc_final: 0.7901 (p0) REVERT: B 498 ARG cc_start: 0.8680 (mtt-85) cc_final: 0.8243 (mtt-85) REVERT: C 26 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.6929 (ttp80) REVERT: D 6 GLN cc_start: 0.8646 (pt0) cc_final: 0.8069 (pt0) REVERT: D 50 TYR cc_start: 0.8137 (p90) cc_final: 0.7883 (p90) REVERT: E 80 TYR cc_start: 0.8053 (m-10) cc_final: 0.7668 (m-10) REVERT: F 4 LEU cc_start: 0.8339 (tp) cc_final: 0.8093 (tp) REVERT: F 48 MET cc_start: 0.7266 (mtt) cc_final: 0.7046 (mtt) outliers start: 17 outliers final: 13 residues processed: 144 average time/residue: 0.0972 time to fit residues: 18.0140 Evaluate side-chains 141 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 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 Chi-restraints excluded: chain F residue 21 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 70 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 7 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.164047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.125678 restraints weight = 8896.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.127606 restraints weight = 7679.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.128764 restraints weight = 6223.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.128930 restraints weight = 5555.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.129225 restraints weight = 5662.299| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6709 Z= 0.152 Angle : 0.606 10.035 9134 Z= 0.303 Chirality : 0.046 0.162 964 Planarity : 0.004 0.039 1176 Dihedral : 4.345 17.748 955 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.28 % Allowed : 19.23 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.30), residues: 814 helix: -3.93 (0.73), residues: 20 sheet: -0.06 (0.30), residues: 272 loop : -0.98 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 67 TYR 0.017 0.001 TYR A 489 PHE 0.017 0.001 PHE A 400 TRP 0.011 0.001 TRP E 50 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 6695) covalent geometry : angle 0.60354 ( 9104) SS BOND : bond 0.00350 ( 12) SS BOND : angle 1.08619 ( 24) hydrogen bonds : bond 0.03157 ( 158) hydrogen bonds : angle 5.44999 ( 444) link_NAG-ASN : bond 0.00058 ( 2) link_NAG-ASN : angle 1.16774 ( 6) *********************** 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 148 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 429 PHE cc_start: 0.7508 (t80) cc_final: 0.7262 (t80) REVERT: A 472 ILE cc_start: 0.9093 (tp) cc_final: 0.8881 (tt) REVERT: B 467 ASP cc_start: 0.8265 (p0) cc_final: 0.7913 (p0) REVERT: D 6 GLN cc_start: 0.8736 (pt0) cc_final: 0.8164 (pt0) REVERT: E 80 TYR cc_start: 0.8108 (m-10) cc_final: 0.7773 (m-10) REVERT: F 119 GLN cc_start: 0.8218 (mp10) cc_final: 0.7846 (mp10) outliers start: 16 outliers final: 14 residues processed: 142 average time/residue: 0.0942 time to fit residues: 17.3523 Evaluate side-chains 139 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 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 21 SER Chi-restraints excluded: chain F residue 39 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 54 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.0010 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.164360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.127256 restraints weight = 8946.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.128545 restraints weight = 7921.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.129296 restraints weight = 6837.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.129651 restraints weight = 6181.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.130117 restraints weight = 6064.964| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6709 Z= 0.146 Angle : 0.602 8.309 9134 Z= 0.304 Chirality : 0.046 0.150 964 Planarity : 0.003 0.039 1176 Dihedral : 4.358 17.291 955 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.28 % Allowed : 19.94 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.30), residues: 814 helix: -4.04 (0.72), residues: 20 sheet: -0.05 (0.30), residues: 272 loop : -1.01 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 80 TYR 0.016 0.001 TYR B 453 PHE 0.016 0.001 PHE A 400 TRP 0.011 0.001 TRP E 50 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6695) covalent geometry : angle 0.60038 ( 9104) SS BOND : bond 0.00339 ( 12) SS BOND : angle 1.02952 ( 24) hydrogen bonds : bond 0.03021 ( 158) hydrogen bonds : angle 5.42614 ( 444) link_NAG-ASN : bond 0.00065 ( 2) link_NAG-ASN : angle 1.14173 ( 6) *********************** 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 148 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 429 PHE cc_start: 0.7507 (t80) cc_final: 0.7240 (t80) REVERT: B 467 ASP cc_start: 0.8246 (p0) cc_final: 0.7927 (p0) REVERT: D 6 GLN cc_start: 0.8767 (pt0) cc_final: 0.8223 (pt0) REVERT: E 80 TYR cc_start: 0.8109 (m-10) cc_final: 0.7804 (m-10) REVERT: F 119 GLN cc_start: 0.8155 (mp10) cc_final: 0.7869 (mp10) outliers start: 16 outliers final: 15 residues processed: 142 average time/residue: 0.0997 time to fit residues: 18.0655 Evaluate side-chains 141 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 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 21 SER Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 93 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 69 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.163302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.125989 restraints weight = 9035.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.127280 restraints weight = 8089.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.127855 restraints weight = 7125.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.128440 restraints weight = 6586.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.128679 restraints weight = 6102.208| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6709 Z= 0.176 Angle : 0.632 8.715 9134 Z= 0.319 Chirality : 0.046 0.155 964 Planarity : 0.004 0.039 1176 Dihedral : 4.484 18.887 955 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.28 % Allowed : 20.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.30), residues: 814 helix: -4.12 (0.72), residues: 20 sheet: -0.21 (0.30), residues: 280 loop : -0.92 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 26 TYR 0.018 0.001 TYR B 453 PHE 0.017 0.001 PHE A 400 TRP 0.015 0.001 TRP E 50 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 6695) covalent geometry : angle 0.62990 ( 9104) SS BOND : bond 0.00350 ( 12) SS BOND : angle 1.17021 ( 24) hydrogen bonds : bond 0.03135 ( 158) hydrogen bonds : angle 5.45512 ( 444) link_NAG-ASN : bond 0.00059 ( 2) link_NAG-ASN : angle 1.12378 ( 6) *********************** 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 147 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 429 PHE cc_start: 0.7512 (t80) cc_final: 0.7239 (t80) REVERT: B 467 ASP cc_start: 0.8258 (p0) cc_final: 0.7928 (p0) REVERT: C 26 ARG cc_start: 0.7701 (mtp-110) cc_final: 0.7460 (mtp85) REVERT: D 6 GLN cc_start: 0.8799 (pt0) cc_final: 0.8270 (pt0) REVERT: E 80 TYR cc_start: 0.8167 (m-10) cc_final: 0.7886 (m-10) REVERT: F 119 GLN cc_start: 0.8160 (mp10) cc_final: 0.7898 (mp10) outliers start: 16 outliers final: 15 residues processed: 140 average time/residue: 0.0926 time to fit residues: 16.8061 Evaluate side-chains 145 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 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 21 SER Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 0.0770 chunk 4 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 0.1980 chunk 35 optimal weight: 0.2980 chunk 73 optimal weight: 3.9990 chunk 75 optimal weight: 0.0870 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 overall best weight: 0.2716 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.163838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.146162 restraints weight = 8854.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.144804 restraints weight = 15599.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.144049 restraints weight = 16338.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.143298 restraints weight = 15194.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.143338 restraints weight = 13843.814| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2503 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= 0.116 Angle : 0.616 8.875 9134 Z= 0.308 Chirality : 0.046 0.156 964 Planarity : 0.004 0.038 1176 Dihedral : 4.220 20.381 955 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.71 % Allowed : 20.66 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.30), residues: 814 helix: -4.33 (0.55), residues: 26 sheet: -0.02 (0.30), residues: 270 loop : -0.97 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 26 TYR 0.014 0.001 TYR B 495 PHE 0.015 0.001 PHE A 400 TRP 0.009 0.001 TRP E 113 HIS 0.002 0.000 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6695) covalent geometry : angle 0.61426 ( 9104) SS BOND : bond 0.00344 ( 12) SS BOND : angle 1.02537 ( 24) hydrogen bonds : bond 0.02732 ( 158) hydrogen bonds : angle 5.31411 ( 444) link_NAG-ASN : bond 0.00104 ( 2) link_NAG-ASN : angle 1.11758 ( 6) ********************** 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 150 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: B 386 LYS cc_start: 0.5296 (pttt) cc_final: 0.4198 (tttt) REVERT: B 425 LEU cc_start: 0.8882 (mt) cc_final: 0.8618 (mt) REVERT: B 467 ASP cc_start: 0.8190 (p0) cc_final: 0.7924 (p0) REVERT: D 6 GLN cc_start: 0.8525 (pt0) cc_final: 0.8139 (pt0) REVERT: E 50 TRP cc_start: 0.9156 (p90) cc_final: 0.8641 (p90) REVERT: E 80 TYR cc_start: 0.8111 (m-10) cc_final: 0.7853 (m-10) REVERT: E 82 GLU cc_start: 0.5884 (mm-30) cc_final: 0.5571 (mp0) outliers start: 12 outliers final: 12 residues processed: 146 average time/residue: 0.0955 time to fit residues: 18.1109 Evaluate side-chains 147 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 5.9990 chunk 66 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.0970 chunk 59 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 E 35 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.165466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.135076 restraints weight = 8890.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.135384 restraints weight = 13502.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.137157 restraints weight = 11415.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.137581 restraints weight = 7458.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.138252 restraints weight = 7459.580| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6709 Z= 0.137 Angle : 0.641 10.703 9134 Z= 0.322 Chirality : 0.046 0.150 964 Planarity : 0.004 0.038 1176 Dihedral : 4.210 20.043 955 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.29), residues: 814 helix: -4.53 (0.40), residues: 38 sheet: 0.01 (0.30), residues: 270 loop : -1.01 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 80 TYR 0.016 0.001 TYR B 489 PHE 0.025 0.001 PHE A 429 TRP 0.012 0.001 TRP E 50 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 6695) covalent geometry : angle 0.63896 ( 9104) SS BOND : bond 0.00324 ( 12) SS BOND : angle 1.05858 ( 24) hydrogen bonds : bond 0.02823 ( 158) hydrogen bonds : angle 5.27945 ( 444) link_NAG-ASN : bond 0.00067 ( 2) link_NAG-ASN : angle 1.06659 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1261.85 seconds wall clock time: 22 minutes 26.00 seconds (1346.00 seconds total)