Starting phenix.real_space_refine on Thu Jul 2 12:38:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bpg_16152/07_2026/8bpg_16152.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bpg_16152/07_2026/8bpg_16152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bpg_16152/07_2026/8bpg_16152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bpg_16152/07_2026/8bpg_16152.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8bpg_16152/07_2026/8bpg_16152.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bpg_16152/07_2026/8bpg_16152.cif" model { file = "/net/cci-nas-00/data/ceres_data/8bpg_16152/07_2026/8bpg_16152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bpg_16152/07_2026/8bpg_16152.cif" } resolution = 3.1 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 5444 2.51 5 N 1468 2.21 5 O 1692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8650 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 797 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "C" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" 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 chiralities: 1 Restraints were copied for chains: A, E, F, H Time building chain proxies: 2.00, per 1000 atoms: 0.23 Number of scatterers: 8650 At special positions: 0 Unit cell: (117.72, 124.2, 102.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 1692 8.00 N 1468 7.00 C 5444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 58 " distance=2.03 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 426 " distance=2.05 Simple disulfide: pdb=" SG CYS D 414 " - pdb=" SG CYS C 414 " distance=2.17 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 536 " distance=2.04 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 426 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.03 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 104 " distance=2.03 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 58 " distance=2.03 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 426 " distance=2.05 Simple disulfide: pdb=" SG CYS E 414 " - pdb=" SG CYS F 414 " distance=2.10 Simple disulfide: pdb=" SG CYS E 474 " - pdb=" SG CYS E 536 " distance=2.04 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 426 " distance=2.03 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 536 " 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 BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG C 601 " - " ASN C 563 " " NAG F 601 " - " ASN F 563 " " NAG G 1 " - " ASN D 563 " " NAG H 1 " - " ASN E 563 " Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 508.1 milliseconds 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 26 sheets defined 11.9% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'B' and resid 69 through 73 Processing helix chain 'D' and resid 353 through 361 Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.815A pdb=" N TRP D 418 " --> pdb=" O CYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 466 removed outlier: 3.765A pdb=" N ASN D 465 " --> pdb=" O GLU D 462 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU D 466 " --> pdb=" O GLN D 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 462 through 466' Processing helix chain 'D' and resid 496 through 498 No H-bonds generated for 'chain 'D' and resid 496 through 498' Processing helix chain 'D' and resid 524 through 530 Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 414 through 420 removed outlier: 3.604A pdb=" N TRP C 418 " --> pdb=" O CYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 466 Processing helix chain 'C' and resid 525 through 530 Processing helix chain 'A' and resid 69 through 73 Processing helix chain 'E' and resid 353 through 361 Processing helix chain 'E' and resid 414 through 421 removed outlier: 3.815A pdb=" N TRP E 418 " --> pdb=" O CYS E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 466 removed outlier: 3.764A pdb=" N ASN E 465 " --> pdb=" O GLU E 462 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU E 466 " --> pdb=" O GLN E 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 462 through 466' Processing helix chain 'E' and resid 496 through 498 No H-bonds generated for 'chain 'E' and resid 496 through 498' Processing helix chain 'E' and resid 524 through 530 Processing helix chain 'F' and resid 353 through 361 Processing helix chain 'F' and resid 414 through 420 removed outlier: 3.603A pdb=" N TRP F 418 " --> pdb=" O CYS F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 466 Processing helix chain 'F' and resid 525 through 530 Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 38 removed outlier: 3.507A pdb=" N CYS B 37 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU B 86 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR B 81 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 48 Processing sheet with id=AA3, first strand: chain 'D' and resid 346 through 350 removed outlier: 3.552A pdb=" N ARG D 346 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR D 366 " --> pdb=" O ILE D 350 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 380 through 384 removed outlier: 3.528A pdb=" N CYS D 426 " --> pdb=" O GLN D 439 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN D 439 " --> pdb=" O CYS D 426 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL D 428 " --> pdb=" O LEU D 437 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 399 through 400 removed outlier: 3.756A pdb=" N THR D 404 " --> pdb=" O HIS D 400 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 453 through 457 removed outlier: 6.094A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 453 through 457 removed outlier: 6.094A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 493 through 494 Processing sheet with id=AA9, first strand: chain 'C' and resid 346 through 350 removed outlier: 3.767A pdb=" N ARG C 346 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR C 366 " --> pdb=" O ILE C 350 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 379 through 383 removed outlier: 3.866A pdb=" N THR C 379 " --> pdb=" O THR C 429 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE C 424 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE C 441 " --> pdb=" O PHE C 424 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 453 through 457 removed outlier: 5.142A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 453 through 457 removed outlier: 5.142A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 485 through 489 removed outlier: 3.604A pdb=" N THR C 535 " --> pdb=" O MET C 489 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 32 through 38 removed outlier: 3.507A pdb=" N CYS A 37 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU A 86 " --> pdb=" O TYR A 81 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR A 81 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 46 through 48 Processing sheet with id=AB7, first strand: chain 'E' and resid 346 through 350 removed outlier: 3.552A pdb=" N ARG E 346 " --> pdb=" O THR E 370 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR E 366 " --> pdb=" O ILE E 350 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 380 through 384 removed outlier: 3.528A pdb=" N CYS E 426 " --> pdb=" O GLN E 439 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN E 439 " --> pdb=" O CYS E 426 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL E 428 " --> pdb=" O LEU E 437 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 399 through 400 removed outlier: 3.756A pdb=" N THR E 404 " --> pdb=" O HIS E 400 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 453 through 457 removed outlier: 6.094A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 453 through 457 removed outlier: 6.094A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 493 through 494 Processing sheet with id=AC4, first strand: chain 'F' and resid 346 through 350 removed outlier: 3.767A pdb=" N ARG F 346 " --> pdb=" O THR F 370 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR F 366 " --> pdb=" O ILE F 350 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 379 through 383 removed outlier: 3.865A pdb=" N THR F 379 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE F 424 " --> pdb=" O ILE F 441 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE F 441 " --> pdb=" O PHE F 424 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 453 through 457 removed outlier: 5.142A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 453 through 457 removed outlier: 5.142A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 485 through 489 removed outlier: 3.606A pdb=" N THR F 535 " --> pdb=" O MET F 489 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 786 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: 1.21 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2096 1.33 - 1.45: 1768 1.45 - 1.58: 4924 1.58 - 1.70: 0 1.70 - 1.82: 64 Bond restraints: 8852 Sorted by residual: bond pdb=" N VAL C 547 " pdb=" CA VAL C 547 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.14e-02 7.69e+03 1.34e+01 bond pdb=" N VAL F 547 " pdb=" CA VAL F 547 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.14e-02 7.69e+03 1.29e+01 bond pdb=" N VAL F 523 " pdb=" CA VAL F 523 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.15e-02 7.56e+03 1.07e+01 bond pdb=" N VAL A 62 " pdb=" CA VAL A 62 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.11e-02 8.12e+03 1.07e+01 bond pdb=" N VAL C 523 " pdb=" CA VAL C 523 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.15e-02 7.56e+03 1.05e+01 ... (remaining 8847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 9252 1.22 - 2.44: 2203 2.44 - 3.66: 565 3.66 - 4.88: 60 4.88 - 6.10: 10 Bond angle restraints: 12090 Sorted by residual: angle pdb=" CA GLY B 107 " pdb=" C GLY B 107 " pdb=" O GLY B 107 " ideal model delta sigma weight residual 122.29 118.24 4.05 8.10e-01 1.52e+00 2.49e+01 angle pdb=" CA GLY A 107 " pdb=" C GLY A 107 " pdb=" O GLY A 107 " ideal model delta sigma weight residual 122.29 118.25 4.04 8.10e-01 1.52e+00 2.49e+01 angle pdb=" N LEU E 466 " pdb=" CA LEU E 466 " pdb=" C LEU E 466 " ideal model delta sigma weight residual 113.18 108.06 5.12 1.21e+00 6.83e-01 1.79e+01 angle pdb=" N LEU D 466 " pdb=" CA LEU D 466 " pdb=" C LEU D 466 " ideal model delta sigma weight residual 113.18 108.08 5.10 1.21e+00 6.83e-01 1.78e+01 angle pdb=" N ASN F 545 " pdb=" CA ASN F 545 " pdb=" C ASN F 545 " ideal model delta sigma weight residual 112.92 108.09 4.83 1.23e+00 6.61e-01 1.54e+01 ... (remaining 12085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 4806 16.02 - 32.04: 394 32.04 - 48.06: 110 48.06 - 64.08: 28 64.08 - 80.10: 4 Dihedral angle restraints: 5342 sinusoidal: 2114 harmonic: 3228 Sorted by residual: dihedral pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 58 " pdb=" CB CYS A 58 " ideal model delta sinusoidal sigma weight residual -86.00 -143.47 57.47 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CB CYS B 49 " pdb=" SG CYS B 49 " pdb=" SG CYS B 58 " pdb=" CB CYS B 58 " ideal model delta sinusoidal sigma weight residual -86.00 -143.45 57.45 1 1.00e+01 1.00e-02 4.43e+01 dihedral pdb=" CA CYS F 414 " pdb=" C CYS F 414 " pdb=" N GLU F 415 " pdb=" CA GLU F 415 " ideal model delta harmonic sigma weight residual 180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 5339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 1394 0.165 - 0.331: 44 0.331 - 0.496: 0 0.496 - 0.661: 0 0.661 - 0.827: 2 Chirality restraints: 1440 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN D 563 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN E 563 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.39e+01 ... (remaining 1437 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 514 " -0.207 9.50e-02 1.11e+02 9.26e-02 5.28e+00 pdb=" NE ARG C 514 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG C 514 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 514 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 514 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 514 " 0.206 9.50e-02 1.11e+02 9.24e-02 5.24e+00 pdb=" NE ARG F 514 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG F 514 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG F 514 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG F 514 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 50 " 0.187 9.50e-02 1.11e+02 8.39e-02 4.34e+00 pdb=" NE ARG A 50 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 50 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 50 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 50 " 0.006 2.00e-02 2.50e+03 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 3320 2.89 - 3.39: 7484 3.39 - 3.90: 13571 3.90 - 4.40: 14476 4.40 - 4.90: 25320 Nonbonded interactions: 64171 Sorted by model distance: nonbonded pdb=" O SER F 381 " pdb=" OG1 THR F 427 " model vdw 2.391 3.040 nonbonded pdb=" O SER C 381 " pdb=" OG1 THR C 427 " model vdw 2.391 3.040 nonbonded pdb=" OG1 THR C 383 " pdb=" O GLU C 388 " model vdw 2.401 3.040 nonbonded pdb=" OG1 THR F 383 " pdb=" O GLU F 388 " model vdw 2.401 3.040 nonbonded pdb=" OG SER C 353 " pdb=" OG SER C 356 " model vdw 2.432 3.040 ... (remaining 64166 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: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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 individual isotropic 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: 5.870 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.840 Find NCS groups from input model: 0.050 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 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 : 0.010 0.136 8872 Z= 0.714 Angle : 1.194 28.985 12136 Z= 0.828 Chirality : 0.079 0.827 1440 Planarity : 0.008 0.093 1538 Dihedral : 12.978 80.095 3204 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: -0.90 (0.25), residues: 1094 helix: -1.03 (0.46), residues: 114 sheet: 0.86 (0.25), residues: 436 loop : -1.80 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 45 TYR 0.012 0.001 TYR E 500 PHE 0.016 0.002 PHE D 516 TRP 0.014 0.002 TRP C 528 HIS 0.006 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00964 / 0.71 ( 8852) covalent geometry : angle 1.10803 / 0.80 (12090) SS BOND : bond 0.04152 / 2.35 ( 14) SS BOND : angle 8.67483 / 5.60 ( 28) hydrogen bonds : bond 0.22214 / 14.96 ( 240) hydrogen bonds : angle 8.84609 / 6.11 ( 786) link_BETA1-4 : bond 0.01674 / 0.84 ( 2) link_BETA1-4 : angle 3.38065 / 1.09 ( 6) link_NAG-ASN : bond 0.00584 / 0.29 ( 4) link_NAG-ASN : angle 4.96375 / 2.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 560 THR cc_start: 0.6979 (p) cc_final: 0.6749 (p) REVERT: C 463 GLN cc_start: 0.6731 (tt0) cc_final: 0.6483 (tt0) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.1238 time to fit residues: 37.4473 Evaluate side-chains 144 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 38 optimal weight: 0.0670 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN D 510 GLN C 439 GLN C 490 GLN A 43 HIS ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 ASN E 510 GLN F 490 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.090569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.063413 restraints weight = 27416.954| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 4.37 r_work: 0.3122 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8872 Z= 0.161 Angle : 0.688 7.191 12136 Z= 0.355 Chirality : 0.047 0.180 1440 Planarity : 0.004 0.029 1538 Dihedral : 4.207 32.096 1186 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.73 % Allowed : 10.71 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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 are not related in a simple way. whole: -0.47 (0.25), residues: 1094 helix: -1.14 (0.43), residues: 112 sheet: 1.32 (0.25), residues: 426 loop : -1.53 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 50 TYR 0.020 0.001 TYR E 375 PHE 0.013 0.001 PHE D 479 TRP 0.009 0.001 TRP D 528 HIS 0.006 0.002 HIS D 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 8852) covalent geometry : angle 0.68099 / 0.35 (12090) SS BOND : bond 0.00687 / 0.48 ( 14) SS BOND : angle 1.75327 / 1.12 ( 28) hydrogen bonds : bond 0.04657 / 3.19 ( 240) hydrogen bonds : angle 6.53548 / 4.49 ( 786) link_BETA1-4 : bond 0.00609 / 0.30 ( 2) link_BETA1-4 : angle 1.08700 / 0.50 ( 6) link_NAG-ASN : bond 0.00261 / 0.13 ( 4) link_NAG-ASN : angle 1.74740 / 0.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.7815 (mp10) cc_final: 0.7379 (mp10) REVERT: E 489 MET cc_start: 0.8921 (mtp) cc_final: 0.8329 (mmt) REVERT: E 493 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7930 (mm110) REVERT: F 405 PHE cc_start: 0.6959 (t80) cc_final: 0.6387 (t80) REVERT: F 463 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8289 (tp40) REVERT: F 489 MET cc_start: 0.8209 (ttm) cc_final: 0.7836 (mmt) REVERT: F 493 GLN cc_start: 0.8666 (mp10) cc_final: 0.8372 (mp10) outliers start: 17 outliers final: 15 residues processed: 169 average time/residue: 0.1090 time to fit residues: 24.0528 Evaluate side-chains 153 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 376 ASP Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 523 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 HIS ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 439 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.088113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.060820 restraints weight = 27278.637| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 4.41 r_work: 0.3057 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8872 Z= 0.163 Angle : 0.657 7.472 12136 Z= 0.338 Chirality : 0.047 0.180 1440 Planarity : 0.004 0.045 1538 Dihedral : 4.191 25.054 1186 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.08 % Allowed : 13.57 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: -0.49 (0.25), residues: 1094 helix: -1.04 (0.43), residues: 112 sheet: 1.21 (0.24), residues: 436 loop : -1.53 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 491 TYR 0.022 0.001 TYR D 375 PHE 0.017 0.002 PHE D 479 TRP 0.009 0.001 TRP F 488 HIS 0.010 0.002 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 8852) covalent geometry : angle 0.65256 / 0.34 (12090) SS BOND : bond 0.00640 / 0.45 ( 14) SS BOND : angle 1.39208 / 0.90 ( 28) hydrogen bonds : bond 0.04229 / 2.90 ( 240) hydrogen bonds : angle 5.89762 / 4.06 ( 786) link_BETA1-4 : bond 0.00147 / 0.07 ( 2) link_BETA1-4 : angle 1.19202 / 0.52 ( 6) link_NAG-ASN : bond 0.00155 / 0.08 ( 4) link_NAG-ASN : angle 1.36363 / 0.67 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 ARG cc_start: 0.8934 (mmp80) cc_final: 0.8576 (mmp80) REVERT: B 94 LEU cc_start: 0.8945 (tp) cc_final: 0.8732 (tt) REVERT: C 499 LYS cc_start: 0.8463 (ttmm) cc_final: 0.8035 (ttmm) REVERT: C 526 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.7983 (pm20) REVERT: C 527 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8682 (mp0) REVERT: C 553 ASP cc_start: 0.7402 (t0) cc_final: 0.7096 (m-30) REVERT: C 568 MET cc_start: 0.8072 (tmm) cc_final: 0.7859 (tmm) REVERT: A 93 GLN cc_start: 0.8107 (mp10) cc_final: 0.7724 (mp10) REVERT: E 417 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8189 (p0) REVERT: E 489 MET cc_start: 0.8932 (mtp) cc_final: 0.8247 (mmt) REVERT: E 493 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7761 (mm110) REVERT: E 568 MET cc_start: 0.8353 (mmm) cc_final: 0.7981 (mmm) REVERT: F 423 ARG cc_start: 0.7611 (tmm-80) cc_final: 0.7376 (tmm-80) REVERT: F 489 MET cc_start: 0.8380 (ttm) cc_final: 0.7975 (tpp) REVERT: F 499 LYS cc_start: 0.8275 (mttp) cc_final: 0.8030 (mttp) outliers start: 40 outliers final: 22 residues processed: 165 average time/residue: 0.1016 time to fit residues: 22.2140 Evaluate side-chains 152 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 526 GLU Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 379 THR Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 523 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 68 optimal weight: 0.3980 chunk 43 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 70 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.088273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.060974 restraints weight = 27580.857| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 4.42 r_work: 0.3068 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8872 Z= 0.133 Angle : 0.629 10.280 12136 Z= 0.323 Chirality : 0.046 0.196 1440 Planarity : 0.004 0.044 1538 Dihedral : 4.150 26.648 1186 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.57 % Allowed : 15.20 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: -0.48 (0.25), residues: 1094 helix: -0.92 (0.44), residues: 112 sheet: 1.15 (0.25), residues: 418 loop : -1.40 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 461 TYR 0.025 0.001 TYR E 375 PHE 0.010 0.001 PHE D 479 TRP 0.008 0.001 TRP D 528 HIS 0.005 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 8852) covalent geometry : angle 0.62623 / 0.32 (12090) SS BOND : bond 0.00671 / 0.47 ( 14) SS BOND : angle 1.22728 / 0.80 ( 28) hydrogen bonds : bond 0.03687 / 2.55 ( 240) hydrogen bonds : angle 5.52264 / 3.81 ( 786) link_BETA1-4 : bond 0.00188 / 0.09 ( 2) link_BETA1-4 : angle 1.10386 / 0.47 ( 6) link_NAG-ASN : bond 0.00097 / 0.05 ( 4) link_NAG-ASN : angle 1.22237 / 0.61 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 MET cc_start: 0.4938 (tmm) cc_final: 0.4594 (tmm) REVERT: B 51 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8266 (mm-30) REVERT: B 83 ARG cc_start: 0.8919 (mmp80) cc_final: 0.8667 (mmp80) REVERT: B 94 LEU cc_start: 0.8938 (tp) cc_final: 0.8694 (tt) REVERT: C 405 PHE cc_start: 0.7258 (t80) cc_final: 0.6406 (t80) REVERT: A 22 GLU cc_start: 0.8914 (tt0) cc_final: 0.8545 (tp30) REVERT: A 42 MET cc_start: 0.4876 (tmm) cc_final: 0.4618 (tmm) REVERT: A 93 GLN cc_start: 0.8243 (mp10) cc_final: 0.7769 (mp10) REVERT: E 417 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8278 (p0) REVERT: E 489 MET cc_start: 0.8917 (mtp) cc_final: 0.8036 (mmm) REVERT: F 405 PHE cc_start: 0.7308 (t80) cc_final: 0.6418 (t80) REVERT: F 423 ARG cc_start: 0.7652 (tmm-80) cc_final: 0.7428 (tmm-80) REVERT: F 489 MET cc_start: 0.8263 (ttm) cc_final: 0.7764 (mmt) REVERT: F 493 GLN cc_start: 0.8236 (mp10) cc_final: 0.8015 (mp10) REVERT: F 499 LYS cc_start: 0.8303 (mttp) cc_final: 0.7979 (mttp) REVERT: F 510 GLN cc_start: 0.8212 (mp10) cc_final: 0.7967 (mp10) REVERT: F 527 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8556 (mp0) outliers start: 35 outliers final: 21 residues processed: 157 average time/residue: 0.1058 time to fit residues: 21.6446 Evaluate side-chains 148 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 376 ASP Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 527 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 6 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 54 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.084512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.057346 restraints weight = 27934.310| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 4.29 r_work: 0.2987 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 8872 Z= 0.233 Angle : 0.697 8.905 12136 Z= 0.360 Chirality : 0.048 0.155 1440 Planarity : 0.005 0.043 1538 Dihedral : 4.524 27.957 1186 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 4.49 % Allowed : 16.84 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: -0.67 (0.25), residues: 1094 helix: -0.88 (0.46), residues: 100 sheet: 0.87 (0.24), residues: 430 loop : -1.48 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 423 TYR 0.019 0.002 TYR E 500 PHE 0.019 0.002 PHE D 479 TRP 0.009 0.001 TRP D 528 HIS 0.006 0.002 HIS E 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.23 ( 8852) covalent geometry : angle 0.69093 / 0.36 (12090) SS BOND : bond 0.00834 / 0.59 ( 14) SS BOND : angle 1.66606 / 1.10 ( 28) hydrogen bonds : bond 0.04221 / 2.87 ( 240) hydrogen bonds : angle 5.62522 / 3.90 ( 786) link_BETA1-4 : bond 0.00245 / 0.12 ( 2) link_BETA1-4 : angle 1.61376 / 0.69 ( 6) link_NAG-ASN : bond 0.00338 / 0.17 ( 4) link_NAG-ASN : angle 1.47119 / 0.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8879 (tptp) REVERT: B 51 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8346 (mm-30) REVERT: B 83 ARG cc_start: 0.8958 (mmp80) cc_final: 0.8725 (mmp80) REVERT: B 94 LEU cc_start: 0.8940 (tp) cc_final: 0.8708 (tt) REVERT: C 499 LYS cc_start: 0.8614 (ttmm) cc_final: 0.8348 (ttmm) REVERT: A 24 LYS cc_start: 0.8979 (tptp) cc_final: 0.8517 (tptp) REVERT: A 51 GLU cc_start: 0.8946 (tp30) cc_final: 0.8700 (tp30) REVERT: A 93 GLN cc_start: 0.8358 (mp10) cc_final: 0.7824 (mp10) REVERT: E 451 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8796 (ppt90) REVERT: E 489 MET cc_start: 0.8912 (mtp) cc_final: 0.8065 (mmm) REVERT: F 489 MET cc_start: 0.8330 (ttm) cc_final: 0.7805 (mmt) REVERT: F 499 LYS cc_start: 0.8337 (mttp) cc_final: 0.7981 (mttp) REVERT: F 527 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8497 (mp0) REVERT: F 566 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8151 (pp) outliers start: 44 outliers final: 32 residues processed: 157 average time/residue: 0.1026 time to fit residues: 21.3972 Evaluate side-chains 156 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LYS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 515 TYR Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 371 ASP Chi-restraints excluded: chain E residue 376 ASP Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 451 ARG Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 566 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 59 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.085432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.058612 restraints weight = 27774.455| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 4.30 r_work: 0.3018 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8872 Z= 0.149 Angle : 0.642 9.142 12136 Z= 0.328 Chirality : 0.046 0.155 1440 Planarity : 0.004 0.052 1538 Dihedral : 4.425 28.672 1186 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.88 % Allowed : 18.27 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: -0.60 (0.25), residues: 1094 helix: -0.76 (0.47), residues: 100 sheet: 0.87 (0.24), residues: 430 loop : -1.40 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 423 TYR 0.022 0.001 TYR E 375 PHE 0.029 0.002 PHE D 405 TRP 0.010 0.001 TRP D 528 HIS 0.006 0.001 HIS E 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 8852) covalent geometry : angle 0.63906 / 0.33 (12090) SS BOND : bond 0.00630 / 0.44 ( 14) SS BOND : angle 1.11804 / 0.75 ( 28) hydrogen bonds : bond 0.03647 / 2.52 ( 240) hydrogen bonds : angle 5.32114 / 3.69 ( 786) link_BETA1-4 : bond 0.00177 / 0.09 ( 2) link_BETA1-4 : angle 1.18549 / 0.52 ( 6) link_NAG-ASN : bond 0.00140 / 0.07 ( 4) link_NAG-ASN : angle 1.22167 / 0.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8918 (tptp) REVERT: B 51 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8375 (mm-30) REVERT: B 83 ARG cc_start: 0.8947 (mmp80) cc_final: 0.8709 (mmp80) REVERT: B 94 LEU cc_start: 0.8952 (tp) cc_final: 0.8710 (tt) REVERT: C 405 PHE cc_start: 0.7318 (t80) cc_final: 0.6524 (t80) REVERT: C 489 MET cc_start: 0.8075 (tpp) cc_final: 0.7857 (tpp) REVERT: C 499 LYS cc_start: 0.8612 (ttmm) cc_final: 0.8347 (ttmm) REVERT: C 527 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.8716 (mp0) REVERT: C 553 ASP cc_start: 0.7526 (t0) cc_final: 0.7129 (m-30) REVERT: A 24 LYS cc_start: 0.9074 (tptp) cc_final: 0.8740 (tptp) REVERT: A 51 GLU cc_start: 0.8915 (tp30) cc_final: 0.8644 (tp30) REVERT: A 93 GLN cc_start: 0.8400 (mp10) cc_final: 0.7891 (mp10) REVERT: E 451 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8796 (ppt90) REVERT: E 489 MET cc_start: 0.8928 (mtp) cc_final: 0.8099 (mmm) REVERT: F 405 PHE cc_start: 0.7319 (t80) cc_final: 0.6405 (t80) REVERT: F 423 ARG cc_start: 0.7881 (tmm-80) cc_final: 0.7680 (mtp85) REVERT: F 489 MET cc_start: 0.8209 (ttm) cc_final: 0.7764 (mmt) REVERT: F 527 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8609 (mp0) outliers start: 38 outliers final: 31 residues processed: 151 average time/residue: 0.1022 time to fit residues: 20.3706 Evaluate side-chains 155 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LYS Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 376 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 515 TYR Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 376 ASP Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 451 ARG Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 527 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 70 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 84 optimal weight: 0.4980 chunk 94 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 HIS D 510 GLN ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.085481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.058378 restraints weight = 27787.873| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 4.39 r_work: 0.3020 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8872 Z= 0.150 Angle : 0.650 8.815 12136 Z= 0.331 Chirality : 0.046 0.154 1440 Planarity : 0.004 0.035 1538 Dihedral : 4.327 27.596 1186 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.80 % Allowed : 18.37 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: -0.60 (0.25), residues: 1094 helix: -0.72 (0.47), residues: 100 sheet: 0.85 (0.24), residues: 430 loop : -1.39 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 461 TYR 0.017 0.001 TYR B 72 PHE 0.021 0.002 PHE C 405 TRP 0.009 0.001 TRP D 528 HIS 0.005 0.001 HIS E 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 8852) covalent geometry : angle 0.64748 / 0.33 (12090) SS BOND : bond 0.00613 / 0.43 ( 14) SS BOND : angle 1.13692 / 0.76 ( 28) hydrogen bonds : bond 0.03599 / 2.47 ( 240) hydrogen bonds : angle 5.19659 / 3.63 ( 786) link_BETA1-4 : bond 0.00235 / 0.12 ( 2) link_BETA1-4 : angle 1.25186 / 0.55 ( 6) link_NAG-ASN : bond 0.00049 / 0.03 ( 4) link_NAG-ASN : angle 1.21086 / 0.63 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 124 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8915 (tptp) REVERT: B 51 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8386 (mm-30) REVERT: B 83 ARG cc_start: 0.8932 (mmp80) cc_final: 0.8695 (mmp80) REVERT: B 94 LEU cc_start: 0.8974 (tp) cc_final: 0.8748 (tt) REVERT: C 499 LYS cc_start: 0.8659 (ttmm) cc_final: 0.8385 (ttmm) REVERT: C 527 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8751 (mp0) REVERT: A 24 LYS cc_start: 0.9062 (tptp) cc_final: 0.8735 (tptp) REVERT: A 51 GLU cc_start: 0.8946 (tp30) cc_final: 0.8676 (tp30) REVERT: A 93 GLN cc_start: 0.8435 (mp10) cc_final: 0.7920 (mp10) REVERT: E 451 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8803 (ppt90) REVERT: E 489 MET cc_start: 0.8879 (mtp) cc_final: 0.8078 (mmm) REVERT: F 489 MET cc_start: 0.8132 (ttm) cc_final: 0.7664 (mmt) REVERT: F 493 GLN cc_start: 0.8314 (mp10) cc_final: 0.8076 (mp10) REVERT: F 499 LYS cc_start: 0.8357 (mttp) cc_final: 0.7919 (mttp) REVERT: F 527 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8571 (mp0) REVERT: F 566 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8195 (pp) outliers start: 47 outliers final: 35 residues processed: 157 average time/residue: 0.0957 time to fit residues: 20.0737 Evaluate side-chains 160 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 120 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LYS Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 376 ASP Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 376 ASP Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 451 ARG Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 566 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 79 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 99 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 HIS D 510 GLN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.085507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.058519 restraints weight = 27123.705| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 4.33 r_work: 0.3025 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8872 Z= 0.146 Angle : 0.643 8.712 12136 Z= 0.330 Chirality : 0.046 0.153 1440 Planarity : 0.004 0.039 1538 Dihedral : 4.313 27.658 1186 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.80 % Allowed : 18.37 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: -0.57 (0.25), residues: 1094 helix: -0.68 (0.48), residues: 100 sheet: 0.95 (0.24), residues: 436 loop : -1.47 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 461 TYR 0.013 0.001 TYR C 515 PHE 0.019 0.001 PHE D 405 TRP 0.009 0.001 TRP D 528 HIS 0.006 0.001 HIS E 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 8852) covalent geometry : angle 0.64025 / 0.33 (12090) SS BOND : bond 0.00599 / 0.43 ( 14) SS BOND : angle 1.08648 / 0.74 ( 28) hydrogen bonds : bond 0.03514 / 2.42 ( 240) hydrogen bonds : angle 5.13895 / 3.60 ( 786) link_BETA1-4 : bond 0.00244 / 0.12 ( 2) link_BETA1-4 : angle 1.20741 / 0.52 ( 6) link_NAG-ASN : bond 0.00041 / 0.02 ( 4) link_NAG-ASN : angle 1.15530 / 0.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 125 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8968 (tptp) REVERT: B 42 MET cc_start: 0.5553 (mmp) cc_final: 0.4841 (tpp) REVERT: B 51 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8379 (mm-30) REVERT: B 83 ARG cc_start: 0.8930 (mmp80) cc_final: 0.8639 (mmp80) REVERT: B 94 LEU cc_start: 0.8964 (tp) cc_final: 0.8737 (tt) REVERT: C 405 PHE cc_start: 0.7260 (t80) cc_final: 0.6373 (t80) REVERT: C 499 LYS cc_start: 0.8669 (ttmm) cc_final: 0.8398 (ttmm) REVERT: C 527 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8770 (mp0) REVERT: A 24 LYS cc_start: 0.9082 (tptp) cc_final: 0.8802 (tptp) REVERT: A 42 MET cc_start: 0.5632 (tpp) cc_final: 0.5383 (tpp) REVERT: A 51 GLU cc_start: 0.8965 (tp30) cc_final: 0.8709 (tp30) REVERT: A 83 ARG cc_start: 0.9223 (mmp80) cc_final: 0.8871 (mmp80) REVERT: A 90 GLU cc_start: 0.9468 (mt-10) cc_final: 0.9249 (tp30) REVERT: A 93 GLN cc_start: 0.8469 (mp10) cc_final: 0.8018 (mp10) REVERT: E 451 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.8759 (ppt90) REVERT: E 489 MET cc_start: 0.8864 (mtp) cc_final: 0.8072 (mmm) REVERT: F 489 MET cc_start: 0.8113 (ttm) cc_final: 0.7642 (mmt) REVERT: F 493 GLN cc_start: 0.8558 (mp10) cc_final: 0.8187 (mp10) REVERT: F 499 LYS cc_start: 0.8378 (mttp) cc_final: 0.8009 (mttp) REVERT: F 527 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8571 (mp0) REVERT: F 566 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8153 (pp) outliers start: 47 outliers final: 36 residues processed: 155 average time/residue: 0.1057 time to fit residues: 21.5438 Evaluate side-chains 162 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LYS Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 376 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 376 ASP Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 451 ARG Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 525 GLU Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 566 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 70 optimal weight: 0.4980 chunk 16 optimal weight: 7.9990 chunk 91 optimal weight: 0.0870 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 102 optimal weight: 0.0570 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 HIS D 510 GLN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.086290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.059378 restraints weight = 27508.705| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 4.34 r_work: 0.3049 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8872 Z= 0.121 Angle : 0.630 9.018 12136 Z= 0.321 Chirality : 0.045 0.158 1440 Planarity : 0.004 0.041 1538 Dihedral : 4.198 29.243 1186 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.98 % Allowed : 19.08 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: -0.55 (0.25), residues: 1094 helix: -0.68 (0.47), residues: 100 sheet: 0.99 (0.24), residues: 436 loop : -1.48 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 461 TYR 0.013 0.001 TYR C 515 PHE 0.028 0.001 PHE F 405 TRP 0.009 0.001 TRP D 528 HIS 0.009 0.001 HIS D 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 8852) covalent geometry : angle 0.62843 / 0.32 (12090) SS BOND : bond 0.00532 / 0.38 ( 14) SS BOND : angle 0.86801 / 0.60 ( 28) hydrogen bonds : bond 0.03287 / 2.28 ( 240) hydrogen bonds : angle 4.92625 / 3.46 ( 786) link_BETA1-4 : bond 0.00230 / 0.11 ( 2) link_BETA1-4 : angle 1.07835 / 0.48 ( 6) link_NAG-ASN : bond 0.00149 / 0.07 ( 4) link_NAG-ASN : angle 1.04889 / 0.55 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LYS cc_start: 0.9244 (tptp) cc_final: 0.8995 (tptp) REVERT: B 42 MET cc_start: 0.5698 (mmp) cc_final: 0.4951 (tpp) REVERT: B 83 ARG cc_start: 0.8918 (mmp80) cc_final: 0.8619 (mmp80) REVERT: B 94 LEU cc_start: 0.8927 (tp) cc_final: 0.8685 (tt) REVERT: C 405 PHE cc_start: 0.7220 (t80) cc_final: 0.6356 (t80) REVERT: C 499 LYS cc_start: 0.8640 (ttmm) cc_final: 0.8379 (ttmm) REVERT: C 527 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8766 (mp0) REVERT: C 568 MET cc_start: 0.6918 (ppp) cc_final: 0.6241 (ppp) REVERT: A 24 LYS cc_start: 0.9118 (tptp) cc_final: 0.8804 (tptp) REVERT: A 29 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8145 (mt) REVERT: A 42 MET cc_start: 0.5281 (tpp) cc_final: 0.4400 (tpp) REVERT: A 51 GLU cc_start: 0.8946 (tp30) cc_final: 0.8691 (tp30) REVERT: A 93 GLN cc_start: 0.8516 (mp10) cc_final: 0.8083 (mp10) REVERT: E 451 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8716 (ppt90) REVERT: E 489 MET cc_start: 0.8872 (mtp) cc_final: 0.8059 (mmm) REVERT: F 489 MET cc_start: 0.8086 (ttm) cc_final: 0.7598 (mmt) REVERT: F 493 GLN cc_start: 0.8492 (mp10) cc_final: 0.8059 (mp10) REVERT: F 499 LYS cc_start: 0.8387 (mttp) cc_final: 0.8027 (mttp) REVERT: F 527 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8544 (mp0) REVERT: F 566 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8114 (pp) outliers start: 39 outliers final: 33 residues processed: 152 average time/residue: 0.0982 time to fit residues: 19.8303 Evaluate side-chains 155 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 376 ASP Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 376 ASP Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 451 ARG Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 525 GLU Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 566 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 80 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 HIS D 510 GLN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.084776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.057994 restraints weight = 27993.300| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 4.20 r_work: 0.3016 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8872 Z= 0.180 Angle : 0.682 9.455 12136 Z= 0.346 Chirality : 0.046 0.160 1440 Planarity : 0.004 0.047 1538 Dihedral : 4.328 28.125 1186 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 4.29 % Allowed : 19.59 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: -0.59 (0.25), residues: 1094 helix: -0.88 (0.47), residues: 100 sheet: 0.91 (0.24), residues: 436 loop : -1.43 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 83 TYR 0.014 0.001 TYR E 500 PHE 0.020 0.002 PHE D 405 TRP 0.008 0.001 TRP D 528 HIS 0.007 0.001 HIS D 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 ( 8852) covalent geometry : angle 0.67911 / 0.34 (12090) SS BOND : bond 0.00680 / 0.48 ( 14) SS BOND : angle 1.20305 / 0.79 ( 28) hydrogen bonds : bond 0.03662 / 2.52 ( 240) hydrogen bonds : angle 5.08915 / 3.58 ( 786) link_BETA1-4 : bond 0.00214 / 0.11 ( 2) link_BETA1-4 : angle 1.27835 / 0.57 ( 6) link_NAG-ASN : bond 0.00105 / 0.05 ( 4) link_NAG-ASN : angle 1.25409 / 0.65 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 121 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LYS cc_start: 0.9276 (tptp) cc_final: 0.9005 (tptp) REVERT: B 42 MET cc_start: 0.5763 (mmp) cc_final: 0.4981 (tpp) REVERT: B 51 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8245 (mm-30) REVERT: B 83 ARG cc_start: 0.8950 (mmp80) cc_final: 0.8646 (mmp80) REVERT: B 94 LEU cc_start: 0.8891 (tp) cc_final: 0.8632 (tt) REVERT: C 499 LYS cc_start: 0.8677 (ttmm) cc_final: 0.8422 (ttmm) REVERT: C 527 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.8811 (mp0) REVERT: C 568 MET cc_start: 0.6702 (ppp) cc_final: 0.5967 (ppp) REVERT: A 42 MET cc_start: 0.5200 (tpp) cc_final: 0.4898 (tpp) REVERT: A 51 GLU cc_start: 0.8973 (tp30) cc_final: 0.8694 (tp30) REVERT: A 93 GLN cc_start: 0.8553 (mp10) cc_final: 0.8116 (mp10) REVERT: E 451 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8740 (ppt90) REVERT: E 489 MET cc_start: 0.8901 (mtp) cc_final: 0.8034 (mmm) REVERT: F 489 MET cc_start: 0.8149 (ttm) cc_final: 0.7630 (mmt) REVERT: F 493 GLN cc_start: 0.8553 (mp10) cc_final: 0.8202 (mp10) REVERT: F 499 LYS cc_start: 0.8419 (mttp) cc_final: 0.8049 (mttp) REVERT: F 527 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8574 (mp0) REVERT: F 566 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8142 (pp) outliers start: 42 outliers final: 38 residues processed: 149 average time/residue: 0.1046 time to fit residues: 20.7514 Evaluate side-chains 160 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 118 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 376 ASP Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 426 CYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 376 ASP Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 451 ARG Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 348 PHE Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 525 GLU Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 566 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 9 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 85 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 HIS D 510 GLN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.084709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.058085 restraints weight = 27645.247| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 4.15 r_work: 0.3022 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8872 Z= 0.160 Angle : 0.673 9.418 12136 Z= 0.341 Chirality : 0.046 0.158 1440 Planarity : 0.004 0.057 1538 Dihedral : 4.334 27.334 1186 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.29 % Allowed : 19.49 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: -0.58 (0.25), residues: 1094 helix: -0.89 (0.46), residues: 100 sheet: 0.92 (0.24), residues: 436 loop : -1.41 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 83 TYR 0.013 0.001 TYR C 515 PHE 0.029 0.002 PHE C 405 TRP 0.008 0.001 TRP D 528 HIS 0.009 0.001 HIS D 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 ( 8852) covalent geometry : angle 0.67090 / 0.34 (12090) SS BOND : bond 0.00648 / 0.46 ( 14) SS BOND : angle 1.12464 / 0.74 ( 28) hydrogen bonds : bond 0.03545 / 2.45 ( 240) hydrogen bonds : angle 5.05673 / 3.56 ( 786) link_BETA1-4 : bond 0.00305 / 0.15 ( 2) link_BETA1-4 : angle 1.21653 / 0.53 ( 6) link_NAG-ASN : bond 0.00057 / 0.03 ( 4) link_NAG-ASN : angle 1.17286 / 0.62 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2637.85 seconds wall clock time: 45 minutes 38.88 seconds (2738.88 seconds total)