Starting phenix.real_space_refine on Thu Feb 13 05:42:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bpg_16152/02_2025/8bpg_16152.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bpg_16152/02_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_16152/02_2025/8bpg_16152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bpg_16152/02_2025/8bpg_16152.map" model { file = "/net/cci-nas-00/data/ceres_data/8bpg_16152/02_2025/8bpg_16152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bpg_16152/02_2025/8bpg_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.57, per 1000 atoms: 0.76 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: 2.14 Conformation dependent library (CDL) restraints added in 1.1 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: 1.18 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: 2.40 Time building geometry restraints manager: 2.48 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: 0.04 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.470 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.230 ------------------------------------------------------------------------------- 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 : 0.950 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: 0.3247 time to fit residues: 97.2987 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 : 1.134 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.090124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.063125 restraints weight = 27148.280| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 4.37 r_work: 0.3128 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 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 : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 405 PHE cc_start: 0.6919 (t80) cc_final: 0.6480 (t80) REVERT: A 93 GLN cc_start: 0.7819 (mp10) cc_final: 0.7408 (mp10) REVERT: E 489 MET cc_start: 0.8839 (mtp) cc_final: 0.8295 (mmt) REVERT: E 493 GLN cc_start: 0.8278 (mm-40) cc_final: 0.7993 (mm110) REVERT: F 405 PHE cc_start: 0.6885 (t80) cc_final: 0.6321 (t80) REVERT: F 423 ARG cc_start: 0.7578 (tmm-80) cc_final: 0.7373 (tmm-80) REVERT: F 463 GLN cc_start: 0.8573 (tp-100) cc_final: 0.8301 (tp40) REVERT: F 489 MET cc_start: 0.8233 (ttm) cc_final: 0.7972 (mmt) REVERT: F 493 GLN cc_start: 0.8711 (mp10) cc_final: 0.8461 (mp10) outliers start: 19 outliers final: 12 residues processed: 172 average time/residue: 0.2656 time to fit residues: 59.1197 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 : 1.064 ------------------------------------------------------------------------------- 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 21 optimal weight: 0.2980 chunk 37 optimal weight: 0.0670 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.088311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.061153 restraints weight = 27692.061| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 4.46 r_work: 0.3078 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3723 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= 0.204 Angle : 0.619 7.774 12090 Z= 0.319 Chirality : 0.046 0.192 1440 Planarity : 0.004 0.044 1538 Dihedral : 4.351 26.350 1312 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.37 % Allowed : 12.96 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.42 (0.25), residues: 1094 helix: -1.19 (0.42), residues: 112 sheet: 1.37 (0.24), residues: 440 loop : -1.57 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 528 HIS 0.009 0.001 HIS D 430 PHE 0.012 0.001 PHE D 479 TYR 0.017 0.001 TYR D 375 ARG 0.006 0.001 ARG D 491 *********************** 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 175 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 GLU cc_start: 0.8780 (tp30) cc_final: 0.8576 (mm-30) REVERT: B 83 ARG cc_start: 0.8936 (mmp80) cc_final: 0.8573 (mmp80) REVERT: C 526 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8627 (pm20) REVERT: C 527 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8894 (mt-10) REVERT: C 553 ASP cc_start: 0.7213 (t0) cc_final: 0.6959 (m-30) REVERT: C 568 MET cc_start: 0.7981 (tmm) cc_final: 0.7756 (tmm) REVERT: A 93 GLN cc_start: 0.8048 (mp10) cc_final: 0.7635 (mp10) REVERT: E 417 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8032 (p0) REVERT: E 489 MET cc_start: 0.8885 (mtp) cc_final: 0.8231 (mmt) REVERT: E 493 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7840 (mm110) REVERT: F 405 PHE cc_start: 0.7116 (t80) cc_final: 0.6605 (t80) REVERT: F 423 ARG cc_start: 0.7570 (tmm-80) cc_final: 0.7355 (tmm-80) REVERT: F 489 MET cc_start: 0.8361 (ttm) cc_final: 0.8017 (tpp) REVERT: F 499 LYS cc_start: 0.8298 (mttp) cc_final: 0.7817 (mttt) outliers start: 33 outliers final: 17 residues processed: 162 average time/residue: 0.2630 time to fit residues: 55.4613 Evaluate side-chains 146 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 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 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 78 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 414 CYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 9 optimal weight: 0.0970 chunk 5 optimal weight: 0.8980 chunk 87 optimal weight: 0.0470 chunk 72 optimal weight: 0.0770 chunk 45 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 overall best weight: 0.3434 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.088731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.061816 restraints weight = 27779.964| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 4.37 r_work: 0.3122 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8852 Z= 0.174 Angle : 0.599 9.112 12090 Z= 0.307 Chirality : 0.045 0.183 1440 Planarity : 0.004 0.042 1538 Dihedral : 4.066 21.561 1312 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.86 % Allowed : 15.31 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.45 (0.25), residues: 1094 helix: -1.23 (0.42), residues: 114 sheet: 1.22 (0.24), residues: 418 loop : -1.35 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 488 HIS 0.004 0.001 HIS E 430 PHE 0.008 0.001 PHE B 67 TYR 0.023 0.001 TYR E 375 ARG 0.006 0.000 ARG C 461 *********************** 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 164 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.7290 (tptp) REVERT: B 83 ARG cc_start: 0.8883 (mmp80) cc_final: 0.8655 (mmp80) REVERT: B 94 LEU cc_start: 0.8988 (tp) cc_final: 0.8781 (tt) REVERT: D 385 GLN cc_start: 0.8293 (tt0) cc_final: 0.7594 (mt0) REVERT: C 405 PHE cc_start: 0.7171 (t80) cc_final: 0.6338 (t80) REVERT: C 568 MET cc_start: 0.7982 (tmm) cc_final: 0.7628 (ptt) REVERT: A 22 GLU cc_start: 0.8823 (tt0) cc_final: 0.8540 (tp30) REVERT: A 93 GLN cc_start: 0.8254 (mp10) cc_final: 0.7782 (mp10) REVERT: E 417 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.7947 (p0) REVERT: E 489 MET cc_start: 0.8715 (mtp) cc_final: 0.7991 (mmm) REVERT: E 493 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7892 (mm110) REVERT: F 405 PHE cc_start: 0.7298 (t80) cc_final: 0.6897 (t80) REVERT: F 489 MET cc_start: 0.8255 (ttm) cc_final: 0.7922 (tpp) REVERT: F 499 LYS cc_start: 0.8250 (mttp) cc_final: 0.7942 (mttp) REVERT: F 527 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8597 (mp0) REVERT: F 553 ASP cc_start: 0.7915 (p0) cc_final: 0.7542 (t0) outliers start: 28 outliers final: 17 residues processed: 156 average time/residue: 0.2617 time to fit residues: 53.0453 Evaluate side-chains 145 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 408 VAL Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 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 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 417 ASP Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 527 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 78 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.086509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.059465 restraints weight = 27532.803| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 4.42 r_work: 0.3056 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4337 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= 0.244 Angle : 0.627 8.985 12090 Z= 0.321 Chirality : 0.045 0.174 1440 Planarity : 0.005 0.082 1538 Dihedral : 4.057 16.889 1312 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.08 % Allowed : 15.82 % 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: -0.43 (0.25), residues: 1094 helix: -0.85 (0.45), residues: 100 sheet: 1.23 (0.24), residues: 422 loop : -1.44 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 488 HIS 0.004 0.001 HIS E 393 PHE 0.015 0.002 PHE D 479 TYR 0.018 0.001 TYR C 515 ARG 0.007 0.001 ARG C 461 *********************** 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 168 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8666 (tptp) cc_final: 0.8268 (tptp) REVERT: B 51 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8273 (mm-30) REVERT: B 83 ARG cc_start: 0.8966 (mmp80) cc_final: 0.8716 (mmp80) REVERT: B 94 LEU cc_start: 0.8980 (tp) cc_final: 0.8764 (tt) REVERT: D 385 GLN cc_start: 0.8208 (tt0) cc_final: 0.7981 (tt0) REVERT: D 417 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8313 (p0) REVERT: C 405 PHE cc_start: 0.7188 (t80) cc_final: 0.6359 (t80) REVERT: C 527 GLU cc_start: 0.9144 (OUTLIER) cc_final: 0.8596 (mp0) REVERT: A 22 GLU cc_start: 0.8836 (tt0) cc_final: 0.8529 (tp30) REVERT: A 68 ILE cc_start: 0.9304 (mp) cc_final: 0.8923 (mt) REVERT: A 83 ARG cc_start: 0.9119 (mmp80) cc_final: 0.8739 (mmp80) REVERT: A 93 GLN cc_start: 0.8369 (mp10) cc_final: 0.7864 (mp10) REVERT: E 417 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8119 (p0) REVERT: E 489 MET cc_start: 0.8923 (mtp) cc_final: 0.7970 (mmm) REVERT: F 405 PHE cc_start: 0.7393 (t80) cc_final: 0.6967 (t80) REVERT: F 489 MET cc_start: 0.8236 (ttm) cc_final: 0.7718 (mmt) REVERT: F 499 LYS cc_start: 0.8344 (mttp) cc_final: 0.7980 (mttp) REVERT: F 510 GLN cc_start: 0.8217 (mp10) cc_final: 0.7993 (mp10) REVERT: F 527 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8534 (mp0) outliers start: 40 outliers final: 26 residues processed: 155 average time/residue: 0.2689 time to fit residues: 54.8174 Evaluate side-chains 152 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 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 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 417 ASP Chi-restraints excluded: chain E residue 447 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 527 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 chunk 93 optimal weight: 0.0980 chunk 20 optimal weight: 0.0270 chunk 2 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 overall best weight: 0.3638 ------------------------------------------------------------------------------- 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 463 GLN ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.087029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.060284 restraints weight = 27330.041| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 4.34 r_work: 0.3062 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8852 Z= 0.175 Angle : 0.602 8.348 12090 Z= 0.307 Chirality : 0.045 0.174 1440 Planarity : 0.004 0.041 1538 Dihedral : 3.892 13.734 1312 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.57 % Allowed : 17.96 % Favored : 78.47 % 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: -0.40 (0.25), residues: 1094 helix: -0.70 (0.46), residues: 100 sheet: 1.30 (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 0.004 0.001 HIS D 393 PHE 0.031 0.001 PHE D 405 TYR 0.015 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 164 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8812 (tptp) cc_final: 0.8417 (tptp) REVERT: B 83 ARG cc_start: 0.8959 (mmp80) cc_final: 0.8705 (mmp80) REVERT: B 94 LEU cc_start: 0.8963 (tp) cc_final: 0.8741 (tt) REVERT: D 417 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8287 (p0) REVERT: C 405 PHE cc_start: 0.7202 (t80) cc_final: 0.6430 (t80) REVERT: C 527 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8578 (mp0) REVERT: A 22 GLU cc_start: 0.8943 (tt0) cc_final: 0.8489 (tp30) REVERT: A 93 GLN cc_start: 0.8337 (mp10) cc_final: 0.7770 (mp10) REVERT: E 417 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8038 (p0) REVERT: E 489 MET cc_start: 0.8910 (mtp) cc_final: 0.7921 (mmm) REVERT: F 405 PHE cc_start: 0.7319 (t80) cc_final: 0.6929 (t80) REVERT: F 489 MET cc_start: 0.8200 (ttm) cc_final: 0.7687 (mmt) REVERT: F 499 LYS cc_start: 0.8357 (mttp) cc_final: 0.7980 (mttp) REVERT: F 510 GLN cc_start: 0.8217 (mp10) cc_final: 0.8002 (mp10) REVERT: F 527 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8539 (mp0) REVERT: F 566 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8108 (pp) outliers start: 35 outliers final: 24 residues processed: 155 average time/residue: 0.2487 time to fit residues: 50.2608 Evaluate side-chains 150 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 417 ASP Chi-restraints excluded: chain D residue 568 MET Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 78 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 417 ASP 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 527 GLU 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 19 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 103 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.083799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.056619 restraints weight = 28057.261| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 4.40 r_work: 0.2979 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8852 Z= 0.366 Angle : 0.680 8.116 12090 Z= 0.350 Chirality : 0.047 0.154 1440 Planarity : 0.005 0.058 1538 Dihedral : 4.267 21.133 1312 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 4.90 % Allowed : 17.96 % 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: -0.71 (0.25), residues: 1094 helix: -0.93 (0.46), residues: 102 sheet: 0.83 (0.23), residues: 442 loop : -1.54 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 488 HIS 0.009 0.002 HIS A 43 PHE 0.024 0.002 PHE D 405 TYR 0.021 0.002 TYR C 515 ARG 0.008 0.001 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 167 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 119 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8334 (mm-30) REVERT: B 83 ARG cc_start: 0.8952 (mmp80) cc_final: 0.8722 (mmp80) REVERT: B 94 LEU cc_start: 0.8984 (tp) cc_final: 0.8761 (tt) REVERT: D 417 ASP cc_start: 0.8891 (OUTLIER) cc_final: 0.8473 (p0) REVERT: C 527 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.8694 (mp0) REVERT: A 42 MET cc_start: 0.6127 (OUTLIER) cc_final: 0.4611 (tpp) REVERT: A 68 ILE cc_start: 0.9286 (mp) cc_final: 0.8920 (mt) REVERT: A 93 GLN cc_start: 0.8410 (mp10) cc_final: 0.7906 (mp10) REVERT: E 417 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8323 (p0) REVERT: F 489 MET cc_start: 0.8161 (ttm) cc_final: 0.7852 (mtm) REVERT: F 499 LYS cc_start: 0.8368 (mttp) cc_final: 0.8030 (mttp) REVERT: F 527 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8585 (mp0) REVERT: F 566 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8196 (pp) outliers start: 48 outliers final: 33 residues processed: 152 average time/residue: 0.2585 time to fit residues: 51.6327 Evaluate side-chains 153 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 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 417 ASP 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 350 ILE Chi-restraints excluded: chain C residue 363 THR 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 42 MET 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 408 VAL Chi-restraints excluded: chain E residue 414 CYS Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 447 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 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 34 optimal weight: 3.9990 chunk 102 optimal weight: 0.0170 chunk 104 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 26 optimal weight: 0.0470 chunk 61 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 28 optimal weight: 0.0470 overall best weight: 0.3414 ------------------------------------------------------------------------------- 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 ** D 400 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 = 0.3829 r_free = 0.3829 target = 0.085629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.058595 restraints weight = 27872.926| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 4.44 r_work: 0.3030 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4979 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= 0.184 Angle : 0.632 8.842 12090 Z= 0.325 Chirality : 0.045 0.176 1440 Planarity : 0.005 0.120 1538 Dihedral : 4.041 24.786 1312 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.08 % Allowed : 19.08 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.70 (0.47), residues: 100 sheet: 1.20 (0.24), residues: 426 loop : -1.52 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 528 HIS 0.014 0.001 HIS D 400 PHE 0.029 0.002 PHE C 405 TYR 0.016 0.001 TYR C 515 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 164 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 51 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8300 (mm-30) REVERT: B 83 ARG cc_start: 0.8918 (mmp80) cc_final: 0.8620 (mmp80) REVERT: B 94 LEU cc_start: 0.8963 (tp) cc_final: 0.8728 (tt) REVERT: B 123 HIS cc_start: 0.7797 (m-70) cc_final: 0.6587 (m-70) REVERT: D 417 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8436 (p0) REVERT: C 405 PHE cc_start: 0.7137 (t80) cc_final: 0.6319 (t80) REVERT: C 527 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8616 (mp0) REVERT: A 22 GLU cc_start: 0.9034 (tt0) cc_final: 0.8608 (tp30) REVERT: A 42 MET cc_start: 0.5905 (tpp) cc_final: 0.4772 (tpp) REVERT: A 68 ILE cc_start: 0.9261 (mp) cc_final: 0.8886 (mt) REVERT: A 93 GLN cc_start: 0.8489 (mp10) cc_final: 0.8006 (mp10) REVERT: E 417 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8201 (p0) REVERT: E 451 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8835 (ppt90) REVERT: E 489 MET cc_start: 0.8876 (mtp) cc_final: 0.8161 (mmm) REVERT: E 493 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7824 (tp40) REVERT: F 405 PHE cc_start: 0.7289 (t80) cc_final: 0.6545 (t80) REVERT: F 489 MET cc_start: 0.8181 (ttm) cc_final: 0.7642 (mmt) REVERT: F 499 LYS cc_start: 0.8316 (mttp) cc_final: 0.7988 (mttp) REVERT: F 527 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8518 (mp0) REVERT: F 566 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8168 (pp) outliers start: 40 outliers final: 29 residues processed: 152 average time/residue: 0.2557 time to fit residues: 51.0451 Evaluate side-chains 154 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 408 VAL Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain D residue 417 ASP 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 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 373 THR Chi-restraints excluded: chain E residue 376 ASP Chi-restraints excluded: chain E residue 414 CYS 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 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 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 72 optimal weight: 3.9990 chunk 10 optimal weight: 0.0370 chunk 105 optimal weight: 0.9990 chunk 32 optimal weight: 0.0470 chunk 90 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 HIS D 400 HIS D 510 GLN ** 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 = 0.3831 r_free = 0.3831 target = 0.085646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.058733 restraints weight = 27680.183| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 4.39 r_work: 0.3033 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8852 Z= 0.198 Angle : 0.638 9.175 12090 Z= 0.326 Chirality : 0.045 0.172 1440 Planarity : 0.005 0.093 1538 Dihedral : 3.942 26.240 1312 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.57 % Allowed : 20.31 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.76 (0.47), residues: 102 sheet: 1.21 (0.24), residues: 422 loop : -1.51 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 528 HIS 0.009 0.001 HIS D 400 PHE 0.027 0.002 PHE C 405 TYR 0.014 0.001 TYR C 515 ARG 0.011 0.001 ARG A 83 *********************** 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 157 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: B 51 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8401 (mm-30) REVERT: B 83 ARG cc_start: 0.8931 (mmp80) cc_final: 0.8623 (mmp80) REVERT: B 94 LEU cc_start: 0.9000 (tp) cc_final: 0.8747 (tt) REVERT: D 417 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8436 (p0) REVERT: D 445 LYS cc_start: 0.8822 (tppt) cc_final: 0.8489 (tppt) REVERT: A 22 GLU cc_start: 0.9074 (tt0) cc_final: 0.8619 (tp30) REVERT: A 42 MET cc_start: 0.5938 (tpp) cc_final: 0.4699 (tpp) REVERT: A 93 GLN cc_start: 0.8480 (mp10) cc_final: 0.7981 (mp10) REVERT: E 417 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8248 (p0) REVERT: E 451 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.8690 (ppt90) REVERT: E 489 MET cc_start: 0.8961 (mtp) cc_final: 0.8153 (mmm) REVERT: E 493 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7798 (tp40) REVERT: F 489 MET cc_start: 0.8223 (ttm) cc_final: 0.7569 (mmt) REVERT: F 499 LYS cc_start: 0.8348 (mttp) cc_final: 0.7995 (mttp) REVERT: F 527 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8518 (mp0) REVERT: F 566 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8092 (pp) outliers start: 35 outliers final: 28 residues processed: 146 average time/residue: 0.2642 time to fit residues: 50.6807 Evaluate side-chains 149 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 408 VAL Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain D residue 417 ASP 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 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 417 ASP Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 451 ARG 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 527 GLU 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 67 optimal weight: 0.0970 chunk 12 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 77 optimal weight: 0.1980 chunk 88 optimal weight: 0.9990 chunk 102 optimal weight: 0.0070 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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** ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.085629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.059073 restraints weight = 28280.716| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 4.23 r_work: 0.3044 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8852 Z= 0.189 Angle : 0.631 9.286 12090 Z= 0.322 Chirality : 0.045 0.170 1440 Planarity : 0.005 0.086 1538 Dihedral : 3.902 24.222 1312 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.78 % Allowed : 20.31 % Favored : 75.92 % 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: -0.74 (0.47), residues: 102 sheet: 1.16 (0.24), residues: 426 loop : -1.48 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 528 HIS 0.010 0.001 HIS D 400 PHE 0.016 0.001 PHE D 405 TYR 0.013 0.001 TYR C 515 ARG 0.014 0.001 ARG A 83 ********************** 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 157 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 120 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: B 51 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8408 (mm-30) REVERT: B 52 MET cc_start: 0.7767 (tpt) cc_final: 0.7483 (tmm) REVERT: B 83 ARG cc_start: 0.8912 (mmp80) cc_final: 0.8604 (mmp80) REVERT: B 94 LEU cc_start: 0.8996 (tp) cc_final: 0.8713 (tt) REVERT: D 417 ASP cc_start: 0.8837 (OUTLIER) cc_final: 0.8440 (p0) REVERT: D 445 LYS cc_start: 0.8828 (tppt) cc_final: 0.8577 (tppt) REVERT: C 405 PHE cc_start: 0.7222 (t80) cc_final: 0.6358 (t80) REVERT: C 527 GLU cc_start: 0.9133 (OUTLIER) cc_final: 0.8655 (mp0) REVERT: A 22 GLU cc_start: 0.9065 (tt0) cc_final: 0.8594 (tp30) REVERT: A 42 MET cc_start: 0.6001 (tpp) cc_final: 0.4541 (tpp) REVERT: A 93 GLN cc_start: 0.8440 (mp10) cc_final: 0.8028 (mp10) REVERT: E 417 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8260 (p0) REVERT: E 451 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8669 (ppt90) REVERT: E 489 MET cc_start: 0.8953 (mtp) cc_final: 0.8200 (mmm) REVERT: E 493 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7819 (tp40) REVERT: F 405 PHE cc_start: 0.7184 (t80) cc_final: 0.6212 (t80) REVERT: F 489 MET cc_start: 0.8199 (ttm) cc_final: 0.7559 (mmt) REVERT: F 499 LYS cc_start: 0.8351 (mttp) cc_final: 0.8007 (mttp) REVERT: F 527 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8510 (mp0) REVERT: F 566 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8087 (pp) outliers start: 37 outliers final: 30 residues processed: 146 average time/residue: 0.2537 time to fit residues: 48.9888 Evaluate side-chains 152 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 350 ILE Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 376 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain D residue 417 ASP 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 518 HIS 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 36 LYS Chi-restraints excluded: chain A residue 86 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 414 CYS 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 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 527 GLU 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 8 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 61 optimal weight: 0.0980 chunk 35 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 86 optimal weight: 0.0970 chunk 82 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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** A 123 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.086032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.058987 restraints weight = 27669.554| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 4.42 r_work: 0.3037 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8852 Z= 0.194 Angle : 0.635 10.391 12090 Z= 0.323 Chirality : 0.045 0.168 1440 Planarity : 0.005 0.080 1538 Dihedral : 3.833 24.464 1312 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.88 % Allowed : 20.20 % Favored : 75.92 % 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: -0.45 (0.25), residues: 1094 helix: -0.73 (0.47), residues: 102 sheet: 1.17 (0.24), residues: 426 loop : -1.44 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 528 HIS 0.009 0.001 HIS D 400 PHE 0.015 0.001 PHE D 405 TYR 0.012 0.001 TYR C 515 ARG 0.013 0.001 ARG A 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5901.13 seconds wall clock time: 105 minutes 3.56 seconds (6303.56 seconds total)