Starting phenix.real_space_refine on Sat Aug 23 00:14:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bpg_16152/08_2025/8bpg_16152.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bpg_16152/08_2025/8bpg_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_16152/08_2025/8bpg_16152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bpg_16152/08_2025/8bpg_16152.map" model { file = "/net/cci-nas-00/data/ceres_data/8bpg_16152/08_2025/8bpg_16152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bpg_16152/08_2025/8bpg_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-2.0-5787/lib/python3.9/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 dihedrals: 6 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: A, E, F, H Time building chain proxies: 2.46, per 1000 atoms: 0.28 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: 0.76 Conformation dependent library (CDL) restraints added in 394.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.38 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: 1.34 Time building geometry restraints manager: 1.03 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: 4920 16.02 - 32.04: 402 32.04 - 48.06: 114 48.06 - 64.08: 28 64.08 - 80.10: 4 Dihedral angle restraints: 5468 sinusoidal: 2240 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 5465 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: 0.02 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: 6.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.040 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 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 : 12.890 80.095 3330 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 aren 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 covalent geometry : bond 0.00964 ( 8852) covalent geometry : angle 1.10803 (12090) SS BOND : bond 0.04152 ( 14) SS BOND : angle 8.67483 ( 28) hydrogen bonds : bond 0.22214 ( 240) hydrogen bonds : angle 8.84609 ( 786) link_BETA1-4 : bond 0.01674 ( 2) link_BETA1-4 : angle 3.38065 ( 6) link_NAG-ASN : bond 0.00584 ( 4) link_NAG-ASN : angle 4.96375 ( 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 : 0.365 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: 0.1481 time to fit residues: 44.3391 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 : 0.347 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3905 r_free = 0.3905 target = 0.090504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.063322 restraints weight = 27422.047| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 4.38 r_work: 0.3120 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3198 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= 0.161 Angle : 0.685 7.082 12136 Z= 0.353 Chirality : 0.047 0.205 1440 Planarity : 0.004 0.028 1538 Dihedral : 4.914 33.251 1312 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.84 % Allowed : 10.51 % Favored : 87.65 % 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 aren not related in a simple way. whole: -0.49 (0.25), residues: 1094 helix: -1.23 (0.43), residues: 112 sheet: 1.30 (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 0.017 0.001 TYR E 375 PHE 0.014 0.001 PHE D 479 TRP 0.010 0.001 TRP D 528 HIS 0.007 0.002 HIS D 400 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 8852) covalent geometry : angle 0.67786 (12090) SS BOND : bond 0.00939 ( 14) SS BOND : angle 1.83560 ( 28) hydrogen bonds : bond 0.04547 ( 240) hydrogen bonds : angle 6.49387 ( 786) link_BETA1-4 : bond 0.00058 ( 2) link_BETA1-4 : angle 1.05493 ( 6) link_NAG-ASN : bond 0.00337 ( 4) link_NAG-ASN : angle 1.71234 ( 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 176 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 405 PHE cc_start: 0.6985 (t80) cc_final: 0.6576 (t80) REVERT: A 93 GLN cc_start: 0.7821 (mp10) cc_final: 0.7390 (mp10) REVERT: E 489 MET cc_start: 0.8927 (mtp) cc_final: 0.8334 (mmt) REVERT: E 493 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7900 (mm110) REVERT: F 405 PHE cc_start: 0.6951 (t80) cc_final: 0.6385 (t80) REVERT: F 463 GLN cc_start: 0.8574 (tp-100) cc_final: 0.8294 (tp40) REVERT: F 489 MET cc_start: 0.8218 (ttm) cc_final: 0.7878 (mmt) REVERT: F 493 GLN cc_start: 0.8704 (mp10) cc_final: 0.8437 (mp10) outliers start: 18 outliers final: 15 residues processed: 169 average time/residue: 0.1284 time to fit residues: 28.0698 Evaluate side-chains 152 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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: 1.9990 chunk 86 optimal weight: 0.4980 chunk 106 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 21 optimal weight: 0.1980 chunk 39 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 439 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.088384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.061139 restraints weight = 27245.606| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 4.43 r_work: 0.3076 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3726 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= 0.152 Angle : 0.650 7.621 12136 Z= 0.334 Chirality : 0.047 0.190 1440 Planarity : 0.004 0.042 1538 Dihedral : 4.563 26.138 1312 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.88 % Allowed : 13.37 % Favored : 82.76 % 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 aren not related in a simple way. whole: -0.57 (0.25), residues: 1094 helix: -1.02 (0.43), residues: 112 sheet: 1.10 (0.24), residues: 420 loop : -1.47 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 491 TYR 0.020 0.001 TYR D 375 PHE 0.015 0.001 PHE D 479 TRP 0.009 0.001 TRP F 488 HIS 0.010 0.002 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 8852) covalent geometry : angle 0.64580 (12090) SS BOND : bond 0.00620 ( 14) SS BOND : angle 1.30029 ( 28) hydrogen bonds : bond 0.04176 ( 240) hydrogen bonds : angle 5.90198 ( 786) link_BETA1-4 : bond 0.00205 ( 2) link_BETA1-4 : angle 1.25361 ( 6) link_NAG-ASN : bond 0.00146 ( 4) link_NAG-ASN : angle 1.36590 ( 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: 38 poor density : 143 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 ARG cc_start: 0.8925 (mmp80) cc_final: 0.8565 (mmp80) REVERT: C 526 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.7954 (pm20) REVERT: C 527 GLU cc_start: 0.9125 (OUTLIER) cc_final: 0.8615 (mp0) REVERT: A 93 GLN cc_start: 0.8048 (mp10) cc_final: 0.7637 (mp10) REVERT: E 413 ILE cc_start: 0.8170 (pt) cc_final: 0.7944 (pt) REVERT: E 489 MET cc_start: 0.8869 (mtp) cc_final: 0.8291 (mmt) REVERT: E 493 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7798 (mm110) REVERT: E 568 MET cc_start: 0.8403 (mmm) cc_final: 0.8059 (mmm) REVERT: F 405 PHE cc_start: 0.7138 (t80) cc_final: 0.6603 (t80) REVERT: F 423 ARG cc_start: 0.7602 (tmm-80) cc_final: 0.7385 (tmm-80) REVERT: F 489 MET cc_start: 0.8340 (ttm) cc_final: 0.8049 (tpp) REVERT: F 499 LYS cc_start: 0.8291 (mttp) cc_final: 0.8016 (mttp) outliers start: 38 outliers final: 22 residues processed: 164 average time/residue: 0.1214 time to fit residues: 26.1125 Evaluate side-chains 153 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 72 optimal weight: 0.9990 chunk 68 optimal weight: 0.0050 chunk 43 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 36 optimal weight: 8.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3865 r_free = 0.3865 target = 0.088227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.060879 restraints weight = 27460.641| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 4.42 r_work: 0.3069 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4096 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= 0.138 Angle : 0.633 10.159 12136 Z= 0.325 Chirality : 0.046 0.180 1440 Planarity : 0.004 0.072 1538 Dihedral : 4.387 26.739 1312 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.88 % Allowed : 15.00 % Favored : 81.12 % 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 aren not related in a simple way. whole: -0.50 (0.25), residues: 1094 helix: -0.88 (0.45), residues: 112 sheet: 1.13 (0.24), residues: 418 loop : -1.41 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 461 TYR 0.024 0.001 TYR E 375 PHE 0.011 0.001 PHE D 479 TRP 0.008 0.001 TRP D 528 HIS 0.006 0.001 HIS E 430 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8852) covalent geometry : angle 0.62989 (12090) SS BOND : bond 0.00552 ( 14) SS BOND : angle 1.28029 ( 28) hydrogen bonds : bond 0.03668 ( 240) hydrogen bonds : angle 5.49325 ( 786) link_BETA1-4 : bond 0.00217 ( 2) link_BETA1-4 : angle 1.18792 ( 6) link_NAG-ASN : bond 0.00099 ( 4) link_NAG-ASN : angle 1.23530 ( 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 175 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 MET cc_start: 0.4870 (tmm) cc_final: 0.4500 (tmm) REVERT: B 51 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8301 (mm-30) REVERT: B 83 ARG cc_start: 0.8942 (mmp80) cc_final: 0.8683 (mmp80) REVERT: B 94 LEU cc_start: 0.8962 (tp) cc_final: 0.8738 (tt) REVERT: C 405 PHE cc_start: 0.7231 (t80) cc_final: 0.6394 (t80) REVERT: C 499 LYS cc_start: 0.8433 (ttmm) cc_final: 0.8113 (ttmm) REVERT: A 22 GLU cc_start: 0.8877 (tt0) cc_final: 0.8554 (tp30) REVERT: A 42 MET cc_start: 0.4654 (tmm) cc_final: 0.4385 (tmm) REVERT: A 93 GLN cc_start: 0.8248 (mp10) cc_final: 0.7772 (mp10) REVERT: E 417 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.8274 (p0) REVERT: E 489 MET cc_start: 0.8929 (mtp) cc_final: 0.8042 (mmm) REVERT: F 423 ARG cc_start: 0.7641 (tmm-80) cc_final: 0.7424 (tmm-80) REVERT: F 489 MET cc_start: 0.8276 (ttm) cc_final: 0.7888 (tpp) REVERT: F 499 LYS cc_start: 0.8316 (mttp) cc_final: 0.7977 (mttp) REVERT: F 510 GLN cc_start: 0.8226 (mp10) cc_final: 0.7985 (mp10) REVERT: F 527 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8593 (mp0) outliers start: 38 outliers final: 24 residues processed: 160 average time/residue: 0.1240 time to fit residues: 25.7821 Evaluate side-chains 152 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 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 379 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 523 VAL 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: 2.9990 chunk 101 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 HIS D 540 HIS ** 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 = 0.3778 r_free = 0.3778 target = 0.082834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.055716 restraints weight = 28133.823| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 4.29 r_work: 0.2947 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 8872 Z= 0.327 Angle : 0.774 8.843 12136 Z= 0.402 Chirality : 0.050 0.152 1440 Planarity : 0.005 0.063 1538 Dihedral : 4.948 28.513 1312 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 5.31 % Allowed : 15.92 % Favored : 78.78 % 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 aren not related in a simple way. whole: -0.90 (0.25), residues: 1094 helix: -1.20 (0.44), residues: 100 sheet: 0.76 (0.24), residues: 434 loop : -1.66 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 461 TYR 0.022 0.002 TYR E 500 PHE 0.027 0.003 PHE D 479 TRP 0.009 0.002 TRP F 488 HIS 0.008 0.002 HIS E 393 Details of bonding type rmsd covalent geometry : bond 0.00773 ( 8852) covalent geometry : angle 0.76648 (12090) SS BOND : bond 0.00960 ( 14) SS BOND : angle 2.02390 ( 28) hydrogen bonds : bond 0.04926 ( 240) hydrogen bonds : angle 5.91895 ( 786) link_BETA1-4 : bond 0.00338 ( 2) link_BETA1-4 : angle 1.88570 ( 6) link_NAG-ASN : bond 0.00449 ( 4) link_NAG-ASN : angle 1.69706 ( 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 176 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 124 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8869 (tptp) REVERT: B 51 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8404 (mm-30) REVERT: B 83 ARG cc_start: 0.8965 (mmp80) cc_final: 0.8717 (mmp80) REVERT: B 94 LEU cc_start: 0.8970 (tp) cc_final: 0.8740 (tt) REVERT: C 499 LYS cc_start: 0.8655 (ttmm) cc_final: 0.8338 (ttmm) REVERT: C 526 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8011 (pm20) REVERT: C 527 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8655 (mp0) REVERT: A 42 MET cc_start: 0.4604 (tmm) cc_final: 0.4309 (tmm) REVERT: A 51 GLU cc_start: 0.8972 (tp30) cc_final: 0.8718 (tp30) REVERT: A 83 ARG cc_start: 0.9137 (mmp80) cc_final: 0.8891 (mmp80) REVERT: A 93 GLN cc_start: 0.8354 (mp10) cc_final: 0.7822 (mp10) REVERT: E 451 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8643 (ppt90) REVERT: E 489 MET cc_start: 0.8947 (mtp) cc_final: 0.8140 (mmm) REVERT: F 423 ARG cc_start: 0.7973 (tmm-80) cc_final: 0.7615 (tmm160) REVERT: F 489 MET cc_start: 0.8352 (ttm) cc_final: 0.8013 (tpp) REVERT: F 499 LYS cc_start: 0.8367 (mttp) cc_final: 0.7997 (mttp) REVERT: F 527 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8575 (mp0) REVERT: F 566 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8150 (pp) outliers start: 52 outliers final: 36 residues processed: 160 average time/residue: 0.1210 time to fit residues: 25.6085 Evaluate side-chains 159 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 117 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LYS 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 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 D residue 568 MET 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 526 GLU 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 24 LYS 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 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 523 VAL 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: 0.5980 chunk 5 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 95 optimal weight: 0.0170 chunk 26 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 34 optimal weight: 6.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.085478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.058363 restraints weight = 27393.135| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 4.34 r_work: 0.3018 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8872 Z= 0.133 Angle : 0.642 9.038 12136 Z= 0.329 Chirality : 0.046 0.188 1440 Planarity : 0.004 0.033 1538 Dihedral : 4.529 29.057 1312 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.78 % Allowed : 18.37 % 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 aren not related in a simple way. whole: -0.71 (0.25), residues: 1094 helix: -0.85 (0.47), residues: 100 sheet: 0.87 (0.24), residues: 434 loop : -1.56 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 461 TYR 0.016 0.001 TYR C 515 PHE 0.034 0.002 PHE D 405 TRP 0.012 0.001 TRP D 528 HIS 0.008 0.001 HIS D 400 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8852) covalent geometry : angle 0.63943 (12090) SS BOND : bond 0.00553 ( 14) SS BOND : angle 1.10380 ( 28) hydrogen bonds : bond 0.03631 ( 240) hydrogen bonds : angle 5.31877 ( 786) link_BETA1-4 : bond 0.00223 ( 2) link_BETA1-4 : angle 1.14605 ( 6) link_NAG-ASN : bond 0.00245 ( 4) link_NAG-ASN : angle 1.31211 ( 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 164 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8910 (tptp) REVERT: B 51 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8389 (mm-30) REVERT: B 83 ARG cc_start: 0.8944 (mmp80) cc_final: 0.8694 (mmp80) REVERT: B 94 LEU cc_start: 0.8946 (tp) cc_final: 0.8726 (tt) REVERT: C 405 PHE cc_start: 0.7363 (t80) cc_final: 0.6493 (t80) REVERT: C 499 LYS cc_start: 0.8659 (ttmm) cc_final: 0.8347 (ttmm) REVERT: C 527 GLU cc_start: 0.9209 (OUTLIER) cc_final: 0.8725 (mp0) REVERT: C 553 ASP cc_start: 0.7405 (t0) cc_final: 0.7155 (m-30) REVERT: A 51 GLU cc_start: 0.8975 (tp30) cc_final: 0.8683 (tp30) REVERT: A 93 GLN cc_start: 0.8414 (mp10) cc_final: 0.7908 (mp10) REVERT: E 451 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8718 (ppt90) REVERT: E 489 MET cc_start: 0.8871 (mtp) cc_final: 0.8001 (mmm) REVERT: F 423 ARG cc_start: 0.7921 (tmm-80) cc_final: 0.7646 (tmm-80) REVERT: F 489 MET cc_start: 0.8201 (ttm) cc_final: 0.7732 (mmt) REVERT: F 493 GLN cc_start: 0.8098 (mp10) cc_final: 0.7810 (mp10) REVERT: F 527 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8610 (mp0) outliers start: 37 outliers final: 29 residues processed: 149 average time/residue: 0.1242 time to fit residues: 24.1727 Evaluate side-chains 152 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 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 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 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 379 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 537 VAL 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: 1.9990 chunk 84 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 HIS D 510 GLN A 123 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.085168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.057912 restraints weight = 27683.223| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 4.36 r_work: 0.3007 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8872 Z= 0.160 Angle : 0.659 8.752 12136 Z= 0.337 Chirality : 0.046 0.178 1440 Planarity : 0.004 0.034 1538 Dihedral : 4.395 28.525 1312 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.59 % Allowed : 18.37 % Favored : 77.04 % 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 aren not related in a simple way. whole: -0.70 (0.25), residues: 1094 helix: -0.76 (0.47), residues: 100 sheet: 0.87 (0.24), residues: 436 loop : -1.58 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 461 TYR 0.018 0.001 TYR B 72 PHE 0.021 0.002 PHE C 405 TRP 0.009 0.001 TRP D 528 HIS 0.007 0.001 HIS D 400 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 8852) covalent geometry : angle 0.65543 (12090) SS BOND : bond 0.00661 ( 14) SS BOND : angle 1.20105 ( 28) hydrogen bonds : bond 0.03703 ( 240) hydrogen bonds : angle 5.25523 ( 786) link_BETA1-4 : bond 0.00274 ( 2) link_BETA1-4 : angle 1.23981 ( 6) link_NAG-ASN : bond 0.00069 ( 4) link_NAG-ASN : angle 1.29922 ( 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 168 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 123 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: B 24 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8966 (tptp) REVERT: B 51 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8420 (mm-30) REVERT: B 83 ARG cc_start: 0.8963 (mmp80) cc_final: 0.8652 (mmp80) REVERT: B 94 LEU cc_start: 0.8957 (tp) cc_final: 0.8735 (tt) REVERT: D 445 LYS cc_start: 0.8725 (tppt) cc_final: 0.8483 (tppt) REVERT: C 499 LYS cc_start: 0.8705 (ttmm) cc_final: 0.8401 (ttmm) REVERT: C 527 GLU cc_start: 0.9233 (OUTLIER) cc_final: 0.8774 (mp0) REVERT: A 51 GLU cc_start: 0.8994 (tp30) cc_final: 0.8706 (tp30) REVERT: A 90 GLU cc_start: 0.9490 (mt-10) cc_final: 0.9246 (tp30) REVERT: A 93 GLN cc_start: 0.8432 (mp10) cc_final: 0.7938 (mp10) REVERT: E 451 ARG cc_start: 0.9218 (OUTLIER) cc_final: 0.8707 (ppt90) REVERT: E 489 MET cc_start: 0.8861 (mtp) cc_final: 0.8067 (mmm) REVERT: F 489 MET cc_start: 0.8178 (ttm) cc_final: 0.7684 (mmt) REVERT: F 499 LYS cc_start: 0.8365 (mttp) cc_final: 0.7913 (mttp) REVERT: F 527 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8577 (mp0) REVERT: F 566 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8216 (pp) outliers start: 45 outliers final: 35 residues processed: 154 average time/residue: 0.1232 time to fit residues: 24.7587 Evaluate side-chains 156 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 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 26 GLU 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 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 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 Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 537 VAL 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: 0.0000 chunk 66 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 97 optimal weight: 0.4980 chunk 99 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3818 r_free = 0.3818 target = 0.085128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.058085 restraints weight = 26996.939| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 4.33 r_work: 0.3013 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8872 Z= 0.149 Angle : 0.661 9.128 12136 Z= 0.338 Chirality : 0.046 0.177 1440 Planarity : 0.004 0.039 1538 Dihedral : 4.334 29.506 1312 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.49 % Allowed : 19.18 % Favored : 76.33 % 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 aren not related in a simple way. whole: -0.65 (0.25), residues: 1094 helix: -0.68 (0.47), residues: 100 sheet: 0.89 (0.24), residues: 436 loop : -1.53 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 461 TYR 0.014 0.001 TYR C 515 PHE 0.027 0.002 PHE F 405 TRP 0.010 0.001 TRP D 528 HIS 0.006 0.001 HIS E 393 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8852) covalent geometry : angle 0.65812 (12090) SS BOND : bond 0.00595 ( 14) SS BOND : angle 1.11622 ( 28) hydrogen bonds : bond 0.03576 ( 240) hydrogen bonds : angle 5.15129 ( 786) link_BETA1-4 : bond 0.00381 ( 2) link_BETA1-4 : angle 1.19569 ( 6) link_NAG-ASN : bond 0.00074 ( 4) link_NAG-ASN : angle 1.22815 ( 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 167 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: B 24 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8991 (tptp) REVERT: B 42 MET cc_start: 0.5572 (mmp) cc_final: 0.4713 (tpp) REVERT: B 51 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8405 (mm-30) REVERT: B 83 ARG cc_start: 0.8957 (mmp80) cc_final: 0.8651 (mmp80) REVERT: B 94 LEU cc_start: 0.8937 (tp) cc_final: 0.8701 (tt) REVERT: D 416 ASP cc_start: 0.9323 (t0) cc_final: 0.9102 (p0) REVERT: C 405 PHE cc_start: 0.7283 (t80) cc_final: 0.6391 (t80) REVERT: C 499 LYS cc_start: 0.8712 (ttmm) cc_final: 0.8415 (ttmm) REVERT: C 527 GLU cc_start: 0.9232 (OUTLIER) cc_final: 0.8784 (mp0) REVERT: C 553 ASP cc_start: 0.7504 (t0) cc_final: 0.7277 (m-30) REVERT: A 51 GLU cc_start: 0.8988 (tp30) cc_final: 0.8687 (tp30) REVERT: A 90 GLU cc_start: 0.9501 (mt-10) cc_final: 0.9253 (tp30) REVERT: A 93 GLN cc_start: 0.8511 (mp10) cc_final: 0.8036 (mp10) REVERT: E 451 ARG cc_start: 0.9223 (OUTLIER) cc_final: 0.8706 (ppt90) REVERT: E 489 MET cc_start: 0.8931 (mtp) cc_final: 0.8101 (mmm) REVERT: F 489 MET cc_start: 0.8122 (ttm) cc_final: 0.7616 (mmt) REVERT: F 499 LYS cc_start: 0.8381 (mttp) cc_final: 0.7925 (mttp) REVERT: F 527 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8562 (mp0) REVERT: F 566 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8175 (pp) outliers start: 44 outliers final: 37 residues processed: 153 average time/residue: 0.1174 time to fit residues: 23.5837 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 : 0.336 ------------------------------------------------------------------------------- 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 363 THR 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 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 373 THR 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 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 Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 537 VAL 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: 0.5980 chunk 16 optimal weight: 3.9990 chunk 91 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 102 optimal weight: 0.0670 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 HIS D 510 GLN D 540 HIS ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.085544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.058675 restraints weight = 27493.097| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 4.35 r_work: 0.3029 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8872 Z= 0.130 Angle : 0.658 8.981 12136 Z= 0.336 Chirality : 0.046 0.175 1440 Planarity : 0.004 0.045 1538 Dihedral : 4.238 28.315 1312 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.78 % Allowed : 19.90 % Favored : 76.33 % 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 aren not related in a simple way. whole: -0.62 (0.25), residues: 1094 helix: -0.62 (0.48), residues: 100 sheet: 0.90 (0.24), residues: 436 loop : -1.51 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 83 TYR 0.014 0.001 TYR C 515 PHE 0.016 0.001 PHE D 405 TRP 0.010 0.001 TRP D 528 HIS 0.009 0.001 HIS D 400 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8852) covalent geometry : angle 0.65604 (12090) SS BOND : bond 0.00543 ( 14) SS BOND : angle 0.99137 ( 28) hydrogen bonds : bond 0.03384 ( 240) hydrogen bonds : angle 5.02039 ( 786) link_BETA1-4 : bond 0.00304 ( 2) link_BETA1-4 : angle 1.13371 ( 6) link_NAG-ASN : bond 0.00115 ( 4) link_NAG-ASN : angle 1.14462 ( 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 161 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8951 (tptp) REVERT: B 42 MET cc_start: 0.5630 (mmp) cc_final: 0.4671 (tpp) REVERT: B 83 ARG cc_start: 0.8940 (mmp80) cc_final: 0.8638 (mmp80) REVERT: B 94 LEU cc_start: 0.8948 (tp) cc_final: 0.8708 (tt) REVERT: D 416 ASP cc_start: 0.9265 (t0) cc_final: 0.8958 (p0) REVERT: C 405 PHE cc_start: 0.7293 (t80) cc_final: 0.6365 (t80) REVERT: C 499 LYS cc_start: 0.8692 (ttmm) cc_final: 0.8408 (ttmm) REVERT: C 553 ASP cc_start: 0.7451 (t0) cc_final: 0.7235 (m-30) REVERT: A 42 MET cc_start: 0.5441 (tpp) cc_final: 0.4842 (tpp) REVERT: A 51 GLU cc_start: 0.8951 (tp30) cc_final: 0.8644 (tp30) REVERT: A 93 GLN cc_start: 0.8516 (mp10) cc_final: 0.8095 (mp10) REVERT: E 451 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8723 (ppt90) REVERT: E 489 MET cc_start: 0.8893 (mtp) cc_final: 0.8114 (mmm) REVERT: F 489 MET cc_start: 0.8051 (ttm) cc_final: 0.7594 (mmt) REVERT: F 527 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8563 (mp0) outliers start: 37 outliers final: 31 residues processed: 148 average time/residue: 0.1226 time to fit residues: 23.6210 Evaluate side-chains 152 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 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 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 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 E residue 350 ILE Chi-restraints excluded: chain E residue 373 THR 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 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 Chi-restraints excluded: chain F residue 527 GLU 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: 0.7980 chunk 94 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 44 optimal weight: 0.3980 chunk 36 optimal weight: 0.0470 chunk 78 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3832 r_free = 0.3832 target = 0.085355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.058647 restraints weight = 27887.944| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 4.16 r_work: 0.3033 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.5262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8872 Z= 0.143 Angle : 0.678 10.813 12136 Z= 0.343 Chirality : 0.046 0.172 1440 Planarity : 0.005 0.051 1538 Dihedral : 4.250 34.330 1312 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.78 % Allowed : 20.10 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 1.25 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.25), residues: 1094 helix: -0.61 (0.47), residues: 100 sheet: 0.86 (0.24), residues: 448 loop : -1.44 (0.27), residues: 546 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 0.028 0.002 PHE F 405 TRP 0.009 0.001 TRP D 528 HIS 0.019 0.002 HIS D 400 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 8852) covalent geometry : angle 0.67622 (12090) SS BOND : bond 0.00573 ( 14) SS BOND : angle 1.00808 ( 28) hydrogen bonds : bond 0.03427 ( 240) hydrogen bonds : angle 5.02270 ( 786) link_BETA1-4 : bond 0.00322 ( 2) link_BETA1-4 : angle 1.15980 ( 6) link_NAG-ASN : bond 0.00115 ( 4) link_NAG-ASN : angle 1.17707 ( 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 155 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8985 (tptp) REVERT: B 42 MET cc_start: 0.5663 (mmp) cc_final: 0.4974 (tpp) REVERT: B 51 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8235 (mm-30) REVERT: B 83 ARG cc_start: 0.8960 (mmp80) cc_final: 0.8644 (mmp80) REVERT: B 94 LEU cc_start: 0.8921 (tp) cc_final: 0.8666 (tt) REVERT: C 405 PHE cc_start: 0.7284 (t80) cc_final: 0.6360 (t80) REVERT: C 499 LYS cc_start: 0.8698 (ttmm) cc_final: 0.8405 (ttmm) REVERT: C 527 GLU cc_start: 0.9228 (OUTLIER) cc_final: 0.8810 (mp0) REVERT: C 553 ASP cc_start: 0.7538 (t0) cc_final: 0.7291 (m-30) REVERT: C 568 MET cc_start: 0.6768 (ppp) cc_final: 0.6098 (ppp) REVERT: A 42 MET cc_start: 0.5490 (tpp) cc_final: 0.4738 (tpp) REVERT: A 51 GLU cc_start: 0.8948 (tp30) cc_final: 0.8665 (tp30) REVERT: A 93 GLN cc_start: 0.8528 (mp10) cc_final: 0.8098 (mp10) REVERT: E 451 ARG cc_start: 0.9230 (OUTLIER) cc_final: 0.8781 (ppt90) REVERT: E 489 MET cc_start: 0.8893 (mtp) cc_final: 0.8071 (mmm) REVERT: F 489 MET cc_start: 0.8078 (ttm) cc_final: 0.7587 (mmt) REVERT: F 527 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8535 (mp0) REVERT: F 566 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8155 (pp) outliers start: 37 outliers final: 32 residues processed: 145 average time/residue: 0.1188 time to fit residues: 22.6735 Evaluate side-chains 155 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 363 THR 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 426 CYS Chi-restraints excluded: chain D residue 433 LEU 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 29 LEU Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 373 THR 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 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 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: 0.5980 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 85 optimal weight: 0.0980 chunk 86 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** 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 = 0.3824 r_free = 0.3824 target = 0.085039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.058232 restraints weight = 27762.603| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 4.20 r_work: 0.3022 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8872 Z= 0.148 Angle : 0.672 10.532 12136 Z= 0.339 Chirality : 0.045 0.173 1440 Planarity : 0.004 0.050 1538 Dihedral : 4.185 28.291 1312 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 4.08 % Allowed : 19.69 % 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 aren not related in a simple way. whole: -0.54 (0.25), residues: 1094 helix: -0.65 (0.47), residues: 100 sheet: 0.84 (0.24), residues: 452 loop : -1.39 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 83 TYR 0.014 0.001 TYR C 515 PHE 0.015 0.001 PHE D 405 TRP 0.009 0.001 TRP D 528 HIS 0.015 0.001 HIS D 400 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 8852) covalent geometry : angle 0.66996 (12090) SS BOND : bond 0.00605 ( 14) SS BOND : angle 1.04604 ( 28) hydrogen bonds : bond 0.03423 ( 240) hydrogen bonds : angle 5.02591 ( 786) link_BETA1-4 : bond 0.00287 ( 2) link_BETA1-4 : angle 1.16542 ( 6) link_NAG-ASN : bond 0.00113 ( 4) link_NAG-ASN : angle 1.20003 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2995.33 seconds wall clock time: 52 minutes 8.69 seconds (3128.69 seconds total)