Starting phenix.real_space_refine on Fri Nov 15 10:04:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpg_16152/11_2024/8bpg_16152.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpg_16152/11_2024/8bpg_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpg_16152/11_2024/8bpg_16152.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpg_16152/11_2024/8bpg_16152.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpg_16152/11_2024/8bpg_16152.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpg_16152/11_2024/8bpg_16152.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8650 Number of models: 1 Model: "" Number of chains: 5 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: "A" 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: "E" 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: D, H, B, F Time building chain proxies: 6.21, per 1000 atoms: 0.72 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=2, symmetry=0 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 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: 2.30 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.47 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: 2.52 Time building geometry restraints manager: 2.52 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: 4907 16.02 - 32.04: 389 32.04 - 48.06: 106 48.06 - 64.08: 26 64.08 - 80.10: 4 Dihedral angle restraints: 5432 sinusoidal: 2204 harmonic: 3228 Sorted by residual: 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 dihedral pdb=" CA CYS C 414 " pdb=" C CYS C 414 " pdb=" N GLU C 415 " pdb=" CA GLU C 415 " ideal model delta harmonic sigma weight residual -180.00 -160.07 -19.93 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CG ARG A 83 " pdb=" CD ARG A 83 " pdb=" NE ARG A 83 " pdb=" CZ ARG A 83 " ideal model delta sinusoidal sigma weight residual 180.00 136.71 43.29 2 1.50e+01 4.44e-03 1.00e+01 ... (remaining 5429 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: 2.03 - 2.60: 54 2.60 - 3.18: 7098 3.18 - 3.75: 12278 3.75 - 4.33: 16814 4.33 - 4.90: 27963 Nonbonded interactions: 64207 Sorted by model distance: nonbonded pdb=" SG CYS B 49 " pdb=" SG CYS B 58 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS A 49 " pdb=" SG CYS A 58 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS B 37 " pdb=" SG CYS B 104 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS A 37 " pdb=" SG CYS A 104 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS F 367 " pdb=" SG CYS F 426 " model vdw 2.033 3.760 ... (remaining 64202 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 345 through 568) selection = chain 'D' selection = chain 'E' selection = (chain 'F' and resid 345 through 568) } 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: 4.440 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.000 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.140 ------------------------------------------------------------------------------- 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 0.052 8852 Z= 0.642 Angle : 1.108 6.099 12090 Z= 0.803 Chirality : 0.079 0.827 1440 Planarity : 0.008 0.093 1538 Dihedral : 12.890 80.095 3330 Min Nonbonded Distance : 2.028 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (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 TRP 0.014 0.002 TRP C 528 HIS 0.006 0.001 HIS A 43 PHE 0.016 0.002 PHE D 516 TYR 0.012 0.001 TYR E 500 ARG 0.003 0.000 ARG B 45 *********************** 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 : 1.001 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: 0.3090 time to fit residues: 92.0891 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 : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.0270 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 0.0060 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 439 GLN F 490 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8852 Z= 0.229 Angle : 0.656 6.919 12090 Z= 0.340 Chirality : 0.046 0.211 1440 Planarity : 0.004 0.026 1538 Dihedral : 4.672 32.998 1312 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.94 % Allowed : 10.71 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.25), residues: 1094 helix: -1.24 (0.43), residues: 112 sheet: 1.31 (0.25), residues: 426 loop : -1.49 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 528 HIS 0.007 0.002 HIS D 400 PHE 0.015 0.002 PHE D 479 TYR 0.018 0.001 TYR E 375 ARG 0.006 0.001 ARG A 50 *********************** 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 179 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 560 THR cc_start: 0.7035 (p) cc_final: 0.6814 (p) outliers start: 19 outliers final: 12 residues processed: 172 average time/residue: 0.2787 time to fit residues: 61.9710 Evaluate side-chains 148 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 414 CYS 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 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 414 CYS 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 54 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8852 Z= 0.267 Angle : 0.644 7.177 12090 Z= 0.332 Chirality : 0.046 0.195 1440 Planarity : 0.004 0.047 1538 Dihedral : 4.489 26.434 1312 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.57 % Allowed : 13.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.25), residues: 1094 helix: -1.19 (0.42), residues: 112 sheet: 1.32 (0.24), residues: 440 loop : -1.61 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 488 HIS 0.010 0.002 HIS D 430 PHE 0.018 0.002 PHE D 479 TYR 0.023 0.001 TYR D 375 ARG 0.005 0.001 ARG D 423 *********************** 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 170 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 560 THR cc_start: 0.7035 (p) cc_final: 0.6819 (p) REVERT: E 568 MET cc_start: 0.7419 (mmm) cc_final: 0.7203 (mmm) outliers start: 35 outliers final: 19 residues processed: 155 average time/residue: 0.2675 time to fit residues: 54.1873 Evaluate side-chains 145 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 414 CYS 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 427 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 371 ASP Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 414 CYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 28 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8852 Z= 0.217 Angle : 0.624 9.512 12090 Z= 0.321 Chirality : 0.046 0.184 1440 Planarity : 0.004 0.042 1538 Dihedral : 4.235 19.227 1312 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.78 % Allowed : 15.00 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.25), residues: 1094 helix: -0.98 (0.43), residues: 102 sheet: 1.17 (0.24), residues: 422 loop : -1.43 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 528 HIS 0.005 0.001 HIS D 393 PHE 0.013 0.001 PHE D 479 TYR 0.026 0.001 TYR E 375 ARG 0.006 0.001 ARG D 491 *********************** 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 170 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 560 THR cc_start: 0.6978 (p) cc_final: 0.6745 (p) outliers start: 37 outliers final: 23 residues processed: 159 average time/residue: 0.2692 time to fit residues: 56.2395 Evaluate side-chains 143 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 414 CYS 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 427 THR 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 120 LEU 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 414 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 537 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.0370 chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 72 optimal weight: 0.0570 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8852 Z= 0.248 Angle : 0.643 8.869 12090 Z= 0.328 Chirality : 0.046 0.176 1440 Planarity : 0.004 0.041 1538 Dihedral : 4.171 17.118 1312 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.21 % Favored : 94.70 % Rotamer: Outliers : 3.78 % Allowed : 16.12 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.25), residues: 1094 helix: -0.95 (0.44), residues: 100 sheet: 1.13 (0.24), residues: 422 loop : -1.48 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 528 HIS 0.005 0.001 HIS E 393 PHE 0.013 0.002 PHE D 479 TYR 0.013 0.001 TYR C 515 ARG 0.007 0.001 ARG C 423 *********************** 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 164 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 560 THR cc_start: 0.6984 (p) cc_final: 0.6754 (p) REVERT: F 566 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7396 (pp) outliers start: 37 outliers final: 26 residues processed: 151 average time/residue: 0.2567 time to fit residues: 50.5892 Evaluate side-chains 145 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 371 ASP Chi-restraints excluded: chain D residue 376 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 414 CYS 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 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 78 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 371 ASP Chi-restraints excluded: chain E residue 376 ASP Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 537 VAL 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 35 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 20 optimal weight: 0.0020 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8852 Z= 0.281 Angle : 0.667 9.613 12090 Z= 0.340 Chirality : 0.047 0.172 1440 Planarity : 0.005 0.078 1538 Dihedral : 4.205 16.392 1312 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.58 % Favored : 94.33 % Rotamer: Outliers : 3.98 % Allowed : 17.96 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.25), residues: 1094 helix: -0.94 (0.45), residues: 102 sheet: 1.06 (0.24), residues: 424 loop : -1.54 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 528 HIS 0.005 0.001 HIS E 393 PHE 0.027 0.002 PHE D 405 TYR 0.014 0.001 TYR C 515 ARG 0.007 0.000 ARG C 461 *********************** 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 162 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 560 THR cc_start: 0.6892 (p) cc_final: 0.6656 (p) REVERT: A 123 HIS cc_start: 0.5605 (m-70) cc_final: 0.4922 (m90) REVERT: F 566 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7492 (pp) outliers start: 39 outliers final: 26 residues processed: 150 average time/residue: 0.2618 time to fit residues: 51.0683 Evaluate side-chains 144 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 371 ASP Chi-restraints excluded: chain D residue 376 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 371 ASP Chi-restraints excluded: chain E residue 376 ASP Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain F residue 566 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.0370 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8852 Z= 0.220 Angle : 0.654 9.160 12090 Z= 0.333 Chirality : 0.046 0.176 1440 Planarity : 0.004 0.040 1538 Dihedral : 4.065 18.390 1312 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.03 % Favored : 94.88 % Rotamer: Outliers : 3.06 % Allowed : 19.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.25), residues: 1094 helix: -0.91 (0.44), residues: 102 sheet: 1.05 (0.24), residues: 430 loop : -1.52 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 528 HIS 0.005 0.001 HIS E 393 PHE 0.024 0.002 PHE F 405 TYR 0.017 0.001 TYR B 72 ARG 0.008 0.000 ARG C 461 *********************** 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 150 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 560 THR cc_start: 0.6892 (p) cc_final: 0.6645 (p) outliers start: 30 outliers final: 25 residues processed: 141 average time/residue: 0.2639 time to fit residues: 48.6352 Evaluate side-chains 138 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 414 CYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 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 376 ASP Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 451 ARG Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 537 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 HIS ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 HIS D 510 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8852 Z= 0.293 Angle : 0.681 9.255 12090 Z= 0.348 Chirality : 0.047 0.168 1440 Planarity : 0.005 0.051 1538 Dihedral : 4.198 20.274 1312 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 4.08 % Allowed : 18.78 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.25), residues: 1094 helix: -0.93 (0.44), residues: 102 sheet: 0.90 (0.24), residues: 436 loop : -1.39 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 528 HIS 0.006 0.001 HIS E 393 PHE 0.019 0.002 PHE D 405 TYR 0.015 0.001 TYR E 500 ARG 0.009 0.001 ARG C 461 *********************** 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 151 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7799 (tptp) REVERT: D 560 THR cc_start: 0.6924 (p) cc_final: 0.6667 (p) REVERT: F 566 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7425 (pp) outliers start: 40 outliers final: 29 residues processed: 140 average time/residue: 0.2567 time to fit residues: 47.2452 Evaluate side-chains 139 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 371 ASP Chi-restraints excluded: chain D residue 376 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 477 THR 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 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 373 THR Chi-restraints excluded: chain E residue 376 ASP Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain F residue 348 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 427 THR 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 90 optimal weight: 3.9990 chunk 97 optimal weight: 0.2980 chunk 99 optimal weight: 0.4980 chunk 58 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 96 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 400 HIS ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8852 Z= 0.212 Angle : 0.680 10.905 12090 Z= 0.343 Chirality : 0.046 0.176 1440 Planarity : 0.004 0.044 1538 Dihedral : 4.135 24.795 1312 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.67 % Favored : 94.24 % Rotamer: Outliers : 3.27 % Allowed : 19.49 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.25), residues: 1094 helix: -0.83 (0.46), residues: 100 sheet: 0.99 (0.24), residues: 442 loop : -1.41 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 528 HIS 0.007 0.001 HIS D 400 PHE 0.037 0.002 PHE C 405 TYR 0.014 0.001 TYR C 515 ARG 0.009 0.001 ARG C 461 *********************** 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 146 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8205 (tptp) cc_final: 0.7878 (tptp) REVERT: D 560 THR cc_start: 0.6838 (p) cc_final: 0.6580 (p) REVERT: C 568 MET cc_start: 0.5780 (pmm) cc_final: 0.5563 (pmm) REVERT: F 566 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7385 (pp) outliers start: 32 outliers final: 29 residues processed: 138 average time/residue: 0.2519 time to fit residues: 46.2137 Evaluate side-chains 141 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 414 CYS Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 477 THR 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 A residue 108 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 376 ASP Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 348 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 537 VAL 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 102 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 48 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 400 HIS ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8852 Z= 0.251 Angle : 0.688 8.870 12090 Z= 0.346 Chirality : 0.046 0.175 1440 Planarity : 0.005 0.042 1538 Dihedral : 4.184 29.784 1312 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.31 % Favored : 93.60 % Rotamer: Outliers : 3.57 % Allowed : 19.49 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.25), residues: 1094 helix: -0.99 (0.44), residues: 100 sheet: 0.90 (0.24), residues: 448 loop : -1.51 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 528 HIS 0.009 0.001 HIS D 400 PHE 0.038 0.002 PHE C 405 TYR 0.013 0.001 TYR E 500 ARG 0.009 0.001 ARG C 461 ********************** 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 152 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8232 (tptp) cc_final: 0.7900 (tptp) REVERT: D 560 THR cc_start: 0.6872 (p) cc_final: 0.6624 (p) REVERT: F 566 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7380 (pp) outliers start: 35 outliers final: 33 residues processed: 143 average time/residue: 0.2470 time to fit residues: 46.7212 Evaluate side-chains 145 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 414 CYS Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 477 THR 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 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 376 ASP Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 348 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 537 VAL 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 91 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 79 optimal weight: 0.0970 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 0.0020 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3822 r_free = 0.3822 target = 0.085141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.058379 restraints weight = 27598.162| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 4.39 r_work: 0.3026 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8852 Z= 0.209 Angle : 0.684 8.943 12090 Z= 0.346 Chirality : 0.046 0.174 1440 Planarity : 0.005 0.040 1538 Dihedral : 4.207 28.550 1312 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.58 % Favored : 94.33 % Rotamer: Outliers : 3.47 % Allowed : 19.59 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.25), residues: 1094 helix: -0.94 (0.45), residues: 100 sheet: 0.90 (0.24), residues: 452 loop : -1.45 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 528 HIS 0.010 0.001 HIS D 400 PHE 0.045 0.002 PHE C 405 TYR 0.013 0.001 TYR C 515 ARG 0.009 0.001 ARG C 461 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2442.54 seconds wall clock time: 44 minutes 59.70 seconds (2699.70 seconds total)