Starting phenix.real_space_refine on Fri May 16 07:21:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9atp_43832/05_2025/9atp_43832.cif Found real_map, /net/cci-nas-00/data/ceres_data/9atp_43832/05_2025/9atp_43832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9atp_43832/05_2025/9atp_43832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9atp_43832/05_2025/9atp_43832.map" model { file = "/net/cci-nas-00/data/ceres_data/9atp_43832/05_2025/9atp_43832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9atp_43832/05_2025/9atp_43832.cif" } resolution = 3.5 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= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1380 atoms to isotropic. 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 52 5.16 5 C 8379 2.51 5 N 2153 2.21 5 O 2420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13004 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3513 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 26, 'TRANS': 411} Chain breaks: 5 Chain: "B" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3498 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 25, 'TRANS': 410} Chain breaks: 5 Chain: "C" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3356 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 24, 'TRANS': 392} Chain breaks: 6 Chain: "D" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 879 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "E" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 879 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "L" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 879 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Time building chain proxies: 8.49, per 1000 atoms: 0.65 Number of scatterers: 13004 At special positions: 0 Unit cell: (138.112, 140.768, 126.603, 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 52 16.00 O 2420 8.00 N 2153 7.00 C 8379 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 162 " distance=2.04 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 297 " distance=2.03 Simple disulfide: pdb=" SG CYS A 332 " - pdb=" SG CYS A 357 " distance=2.03 Simple disulfide: pdb=" SG CYS A 375 " - pdb=" SG CYS A 428 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 521 " distance=2.04 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 162 " distance=2.04 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 297 " distance=2.03 Simple disulfide: pdb=" SG CYS B 332 " - pdb=" SG CYS B 357 " distance=2.03 Simple disulfide: pdb=" SG CYS B 375 " - pdb=" SG CYS B 428 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 162 " distance=2.04 Simple disulfide: pdb=" SG CYS C 287 " - pdb=" SG CYS C 297 " distance=2.03 Simple disulfide: pdb=" SG CYS C 332 " - pdb=" SG CYS C 357 " distance=2.03 Simple disulfide: pdb=" SG CYS C 375 " - pdb=" SG CYS C 428 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 521 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.06 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 95 " 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 Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.6 seconds 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3068 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 26 sheets defined 9.0% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 290 through 300 Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.568A pdb=" N PHE A 367 " --> pdb=" O ILE A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 removed outlier: 3.846A pdb=" N LEU A 383 " --> pdb=" O PRO A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 406 Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 333 through 338 Processing helix chain 'B' and resid 345 through 349 removed outlier: 3.614A pdb=" N TRP B 349 " --> pdb=" O VAL B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 368 removed outlier: 4.030A pdb=" N TYR B 365 " --> pdb=" O TYR B 361 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA B 368 " --> pdb=" O ILE B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 386 removed outlier: 4.096A pdb=" N LEU B 383 " --> pdb=" O PRO B 380 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASN B 384 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP B 385 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU B 386 " --> pdb=" O LEU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 406 removed outlier: 4.495A pdb=" N SER B 404 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 418 Processing helix chain 'C' and resid 290 through 300 Processing helix chain 'C' and resid 333 through 338 removed outlier: 3.760A pdb=" N VAL C 337 " --> pdb=" O PRO C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 368 removed outlier: 3.729A pdb=" N TYR C 365 " --> pdb=" O TYR C 361 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA C 368 " --> pdb=" O ILE C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 383 removed outlier: 3.811A pdb=" N LEU C 383 " --> pdb=" O PRO C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 406 removed outlier: 4.464A pdb=" N SER C 404 " --> pdb=" O ASN C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 418 Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'L' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34 removed outlier: 6.769A pdb=" N VAL A 33 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N LEU A 219 " --> pdb=" O HIS A 203 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N HIS A 203 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N SER A 201 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR A 261 " --> pdb=" O PHE A 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 52 removed outlier: 3.558A pdb=" N VAL A 44 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP A 283 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 165 through 168 Processing sheet with id=AA4, first strand: chain 'A' and resid 350 through 354 removed outlier: 3.889A pdb=" N ASN A 350 " --> pdb=" O SER A 395 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 395 " --> pdb=" O ASN A 350 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN A 390 " --> pdb=" O GLU A 512 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU A 512 " --> pdb=" O ASN A 390 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 448 through 450 Processing sheet with id=AA6, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.561A pdb=" N TYR A 485 " --> pdb=" O TYR A 469 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 23 through 27 removed outlier: 3.583A pdb=" N THR B 26 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N ASN B 58 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR B 265 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N SER B 201 " --> pdb=" O PRO B 221 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N HIS B 203 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 9.650A pdb=" N LEU B 219 " --> pdb=" O HIS B 203 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B 33 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 45 through 52 removed outlier: 3.805A pdb=" N ASP B 283 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 165 through 168 removed outlier: 6.352A pdb=" N ASN B 118 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLY B 100 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU B 237 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 350 through 354 removed outlier: 3.670A pdb=" N ASN B 350 " --> pdb=" O SER B 395 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER B 395 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 448 through 449 Processing sheet with id=AB3, first strand: chain 'C' and resid 24 through 27 removed outlier: 8.018A pdb=" N ASN C 58 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TYR C 265 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE C 197 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP C 224 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE C 199 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU C 220 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N HIS C 203 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N ALA C 218 " --> pdb=" O HIS C 203 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL C 33 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 52 removed outlier: 3.828A pdb=" N ASP C 283 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 102 through 104 Processing sheet with id=AB6, first strand: chain 'C' and resid 131 through 132 removed outlier: 6.543A pdb=" N GLN C 131 " --> pdb=" O SER C 157 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 350 through 354 Processing sheet with id=AB8, first strand: chain 'C' and resid 448 through 450 Processing sheet with id=AB9, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AC1, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.444A pdb=" N GLY D 10 " --> pdb=" O THR D 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.359A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N PHE D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N MET D 34 " --> pdb=" O PHE D 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AC4, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.181A pdb=" N GLY E 10 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N SER E 114 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL E 12 " --> pdb=" O SER E 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.564A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N MET E 34 " --> pdb=" O PHE E 50 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 3 through 7 Processing sheet with id=AC7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.205A pdb=" N GLY L 10 " --> pdb=" O THR L 112 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N SER L 114 " --> pdb=" O GLY L 10 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL L 12 " --> pdb=" O SER L 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'L' and resid 57 through 59 removed outlier: 6.605A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N PHE L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N MET L 34 " --> pdb=" O PHE L 50 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 963 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: 3.77 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4093 1.34 - 1.47: 3549 1.47 - 1.59: 5642 1.59 - 1.71: 0 1.71 - 1.83: 61 Bond restraints: 13345 Sorted by residual: bond pdb=" CB ASP A 194 " pdb=" CG ASP A 194 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.37e+00 bond pdb=" CA LEU B 272 " pdb=" CB LEU B 272 " ideal model delta sigma weight residual 1.528 1.507 0.021 1.51e-02 4.39e+03 1.98e+00 bond pdb=" CA ASP A 194 " pdb=" CB ASP A 194 " ideal model delta sigma weight residual 1.529 1.551 -0.022 1.62e-02 3.81e+03 1.87e+00 bond pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " ideal model delta sigma weight residual 1.808 1.768 0.040 3.30e-02 9.18e+02 1.45e+00 bond pdb=" CD LYS L 64 " pdb=" CE LYS L 64 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.32e+00 ... (remaining 13340 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 17779 2.28 - 4.55: 313 4.55 - 6.83: 37 6.83 - 9.10: 5 9.10 - 11.38: 1 Bond angle restraints: 18135 Sorted by residual: angle pdb=" N GLY L 10 " pdb=" CA GLY L 10 " pdb=" C GLY L 10 " ideal model delta sigma weight residual 110.43 116.02 -5.59 1.35e+00 5.49e-01 1.71e+01 angle pdb=" CB MET L 82 " pdb=" CG MET L 82 " pdb=" SD MET L 82 " ideal model delta sigma weight residual 112.70 124.08 -11.38 3.00e+00 1.11e-01 1.44e+01 angle pdb=" N GLY E 10 " pdb=" CA GLY E 10 " pdb=" C GLY E 10 " ideal model delta sigma weight residual 110.43 115.44 -5.01 1.35e+00 5.49e-01 1.38e+01 angle pdb=" CA GLU A 129 " pdb=" CB GLU A 129 " pdb=" CG GLU A 129 " ideal model delta sigma weight residual 114.10 121.50 -7.40 2.00e+00 2.50e-01 1.37e+01 angle pdb=" N GLY A 100 " pdb=" CA GLY A 100 " pdb=" C GLY A 100 " ideal model delta sigma weight residual 110.56 115.28 -4.72 1.36e+00 5.41e-01 1.20e+01 ... (remaining 18130 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6867 17.95 - 35.90: 818 35.90 - 53.86: 143 53.86 - 71.81: 14 71.81 - 89.76: 12 Dihedral angle restraints: 7854 sinusoidal: 3078 harmonic: 4776 Sorted by residual: dihedral pdb=" CA LYS A 94 " pdb=" C LYS A 94 " pdb=" N SER A 95 " pdb=" CA SER A 95 " ideal model delta harmonic sigma weight residual 180.00 155.40 24.60 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CB CYS B 476 " pdb=" SG CYS B 476 " pdb=" SG CYS B 484 " pdb=" CB CYS B 484 " ideal model delta sinusoidal sigma weight residual 93.00 53.81 39.19 1 1.00e+01 1.00e-02 2.16e+01 dihedral pdb=" CA ALA B 516 " pdb=" C ALA B 516 " pdb=" N PRO B 517 " pdb=" CA PRO B 517 " ideal model delta harmonic sigma weight residual 180.00 -157.63 -22.37 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 7851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1726 0.074 - 0.148: 247 0.148 - 0.222: 10 0.222 - 0.295: 1 0.295 - 0.369: 3 Chirality restraints: 1987 Sorted by residual: chirality pdb=" CB VAL L 63 " pdb=" CA VAL L 63 " pdb=" CG1 VAL L 63 " pdb=" CG2 VAL L 63 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CB THR C 30 " pdb=" CA THR C 30 " pdb=" OG1 THR C 30 " pdb=" CG2 THR C 30 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB ILE E 28 " pdb=" CA ILE E 28 " pdb=" CG1 ILE E 28 " pdb=" CG2 ILE E 28 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 1984 not shown) Planarity restraints: 2326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 101 " 0.026 2.00e-02 2.50e+03 2.81e-02 1.97e+01 pdb=" CG TRP B 101 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP B 101 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP B 101 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 101 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 101 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 101 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 101 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 101 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 101 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 516 " -0.056 5.00e-02 4.00e+02 8.48e-02 1.15e+01 pdb=" N PRO B 517 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO B 517 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 517 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 225 " 0.039 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO C 226 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 226 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 226 " 0.032 5.00e-02 4.00e+02 ... (remaining 2323 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 186 2.61 - 3.19: 11356 3.19 - 3.76: 19072 3.76 - 4.33: 26290 4.33 - 4.90: 43357 Nonbonded interactions: 100261 Sorted by model distance: nonbonded pdb=" OD1 ASP L 99 " pdb=" N LYS L 100 " model vdw 2.043 3.120 nonbonded pdb=" NH2 ARG L 66 " pdb=" O SER L 84 " model vdw 2.133 3.120 nonbonded pdb=" NH2 ARG B 31 " pdb=" O PRO B 213 " model vdw 2.169 3.120 nonbonded pdb=" OE1 GLN C 49 " pdb=" OG1 THR C 270 " model vdw 2.177 3.040 nonbonded pdb=" OH TYR A 88 " pdb=" OE1 GLU A 187 " model vdw 2.209 3.040 ... (remaining 100256 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 62 or resid 83 through 173 or resid 184 through \ 466 or resid 486 through 525)) selection = (chain 'B' and (resid 22 through 62 or resid 83 through 173 or resid 184 through \ 466 or resid 486 through 525)) selection = (chain 'C' and (resid 22 through 62 or resid 83 through 525)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'L' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 31.400 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 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 : 0.005 0.040 13365 Z= 0.216 Angle : 0.731 11.381 18175 Z= 0.396 Chirality : 0.050 0.369 1987 Planarity : 0.005 0.085 2326 Dihedral : 15.179 89.758 4726 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.22 % Favored : 93.47 % Rotamer: Outliers : 0.21 % Allowed : 21.50 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.38 (0.20), residues: 1592 helix: -2.04 (0.48), residues: 103 sheet: 0.37 (0.22), residues: 540 loop : -1.64 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP B 101 HIS 0.020 0.001 HIS A 501 PHE 0.038 0.002 PHE L 67 TYR 0.016 0.002 TYR B 166 ARG 0.008 0.001 ARG B 462 Details of bonding type rmsd hydrogen bonds : bond 0.11307 ( 381) hydrogen bonds : angle 7.20549 ( 963) SS BOND : bond 0.00727 ( 20) SS BOND : angle 1.02484 ( 40) covalent geometry : bond 0.00489 (13345) covalent geometry : angle 0.73022 (18135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 98 VAL cc_start: 0.4089 (t) cc_final: 0.3527 (t) REVERT: D 103 ASP cc_start: 0.4834 (m-30) cc_final: 0.4162 (m-30) outliers start: 3 outliers final: 2 residues processed: 97 average time/residue: 0.2475 time to fit residues: 36.1728 Evaluate side-chains 83 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 474 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 125 optimal weight: 50.0000 chunk 48 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 145 optimal weight: 0.0170 overall best weight: 1.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 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 = 0.4453 r_free = 0.4453 target = 0.157713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.102992 restraints weight = 35198.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.104232 restraints weight = 20264.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.103419 restraints weight = 13716.101| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13365 Z= 0.181 Angle : 0.616 6.876 18175 Z= 0.330 Chirality : 0.047 0.220 1987 Planarity : 0.005 0.064 2326 Dihedral : 4.555 34.244 1780 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.28 % Favored : 93.47 % Rotamer: Outliers : 2.30 % Allowed : 18.93 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.25 (0.21), residues: 1592 helix: -1.84 (0.44), residues: 117 sheet: 0.54 (0.23), residues: 529 loop : -1.58 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 101 HIS 0.007 0.001 HIS A 501 PHE 0.017 0.002 PHE L 67 TYR 0.014 0.001 TYR B 491 ARG 0.006 0.001 ARG D 45 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 381) hydrogen bonds : angle 6.23120 ( 963) SS BOND : bond 0.00287 ( 20) SS BOND : angle 0.93727 ( 40) covalent geometry : bond 0.00418 (13345) covalent geometry : angle 0.61549 (18135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.6948 (OUTLIER) cc_final: 0.6736 (tp) REVERT: B 101 TRP cc_start: 0.7625 (m-90) cc_final: 0.7412 (m-90) REVERT: B 467 GLU cc_start: 0.8850 (tp30) cc_final: 0.8321 (pp20) REVERT: D 46 GLU cc_start: 0.8673 (mm-30) cc_final: 0.7960 (mm-30) REVERT: D 98 VAL cc_start: 0.6113 (t) cc_final: 0.5679 (p) REVERT: L 75 LYS cc_start: 0.9224 (mmmt) cc_final: 0.8924 (mmmm) outliers start: 33 outliers final: 19 residues processed: 111 average time/residue: 0.2407 time to fit residues: 40.1713 Evaluate side-chains 98 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 111 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 43 optimal weight: 6.9990 chunk 117 optimal weight: 0.4980 chunk 138 optimal weight: 50.0000 chunk 142 optimal weight: 0.3980 chunk 146 optimal weight: 0.0980 chunk 88 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 115 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 HIS B 169 GLN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.172770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.119752 restraints weight = 36325.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.119588 restraints weight = 19426.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.119463 restraints weight = 15556.896| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13365 Z= 0.110 Angle : 0.557 6.903 18175 Z= 0.294 Chirality : 0.045 0.195 1987 Planarity : 0.004 0.049 2326 Dihedral : 4.063 20.358 1774 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.40 % Favored : 94.35 % Rotamer: Outliers : 1.81 % Allowed : 19.62 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.03 (0.21), residues: 1592 helix: -1.67 (0.45), residues: 117 sheet: 0.77 (0.22), residues: 540 loop : -1.52 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 101 HIS 0.002 0.000 HIS A 203 PHE 0.012 0.001 PHE A 234 TYR 0.009 0.001 TYR B 200 ARG 0.003 0.000 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.03131 ( 381) hydrogen bonds : angle 5.85086 ( 963) SS BOND : bond 0.00228 ( 20) SS BOND : angle 0.80821 ( 40) covalent geometry : bond 0.00251 (13345) covalent geometry : angle 0.55618 (18135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.6933 (OUTLIER) cc_final: 0.6709 (tp) REVERT: B 101 TRP cc_start: 0.7450 (m-90) cc_final: 0.7168 (m-90) REVERT: B 173 MET cc_start: 0.7187 (ppp) cc_final: 0.6981 (pmm) REVERT: B 265 TYR cc_start: 0.6782 (m-80) cc_final: 0.6388 (m-80) REVERT: B 467 GLU cc_start: 0.8858 (tp30) cc_final: 0.8326 (pp20) REVERT: C 265 TYR cc_start: 0.8110 (m-80) cc_final: 0.7528 (m-80) REVERT: D 38 ARG cc_start: 0.8662 (ptm160) cc_final: 0.8366 (ptm160) REVERT: D 46 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8299 (mp0) REVERT: L 50 PHE cc_start: 0.8534 (m-80) cc_final: 0.8032 (m-80) REVERT: L 75 LYS cc_start: 0.9225 (mmmt) cc_final: 0.8898 (mmmm) REVERT: L 107 GLN cc_start: 0.7899 (mp10) cc_final: 0.7610 (mp10) outliers start: 26 outliers final: 14 residues processed: 113 average time/residue: 0.2466 time to fit residues: 42.0060 Evaluate side-chains 96 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain L residue 102 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 148 optimal weight: 20.0000 chunk 137 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 152 optimal weight: 0.5980 chunk 112 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 HIS D 32 ASN L 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.156336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.102889 restraints weight = 36377.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.101725 restraints weight = 20514.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.101485 restraints weight = 16277.351| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13365 Z= 0.233 Angle : 0.620 7.056 18175 Z= 0.329 Chirality : 0.046 0.195 1987 Planarity : 0.005 0.049 2326 Dihedral : 4.377 19.051 1774 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.47 % Favored : 93.22 % Rotamer: Outliers : 2.99 % Allowed : 19.83 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.23 (0.21), residues: 1592 helix: -1.70 (0.45), residues: 117 sheet: 0.48 (0.23), residues: 529 loop : -1.53 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 101 HIS 0.003 0.001 HIS A 203 PHE 0.017 0.002 PHE A 190 TYR 0.020 0.002 TYR A 156 ARG 0.003 0.000 ARG C 154 Details of bonding type rmsd hydrogen bonds : bond 0.03610 ( 381) hydrogen bonds : angle 5.98608 ( 963) SS BOND : bond 0.00307 ( 20) SS BOND : angle 0.93023 ( 40) covalent geometry : bond 0.00548 (13345) covalent geometry : angle 0.61942 (18135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 77 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 PHE cc_start: 0.6481 (OUTLIER) cc_final: 0.6224 (t80) REVERT: A 430 ILE cc_start: 0.7083 (OUTLIER) cc_final: 0.6748 (tp) REVERT: B 101 TRP cc_start: 0.7693 (m-90) cc_final: 0.7315 (m-90) REVERT: B 211 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8406 (m-30) REVERT: B 410 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8628 (mt0) REVERT: B 467 GLU cc_start: 0.8911 (tp30) cc_final: 0.8284 (pp20) REVERT: B 515 HIS cc_start: 0.6092 (t-90) cc_final: 0.5873 (t-90) REVERT: L 75 LYS cc_start: 0.9226 (mmmt) cc_final: 0.8941 (mmmm) outliers start: 43 outliers final: 27 residues processed: 115 average time/residue: 0.2457 time to fit residues: 42.9510 Evaluate side-chains 99 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 68 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 95 CYS Chi-restraints excluded: chain L residue 102 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 4 optimal weight: 0.5980 chunk 64 optimal weight: 0.0470 chunk 123 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 127 optimal weight: 20.0000 chunk 126 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 136 optimal weight: 20.0000 overall best weight: 1.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 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 = 0.4471 r_free = 0.4471 target = 0.166272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.112685 restraints weight = 35134.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.112437 restraints weight = 21530.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.111676 restraints weight = 16771.394| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13365 Z= 0.153 Angle : 0.573 6.982 18175 Z= 0.300 Chirality : 0.045 0.183 1987 Planarity : 0.004 0.048 2326 Dihedral : 4.194 19.257 1774 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.78 % Favored : 94.03 % Rotamer: Outliers : 2.78 % Allowed : 20.74 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.09 (0.21), residues: 1592 helix: -1.51 (0.47), residues: 111 sheet: 0.64 (0.23), residues: 524 loop : -1.49 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 61 HIS 0.002 0.001 HIS A 501 PHE 0.013 0.001 PHE A 234 TYR 0.016 0.001 TYR A 156 ARG 0.003 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.03166 ( 381) hydrogen bonds : angle 5.78109 ( 963) SS BOND : bond 0.00300 ( 20) SS BOND : angle 0.97299 ( 40) covalent geometry : bond 0.00358 (13345) covalent geometry : angle 0.57173 (18135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 80 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.7162 (OUTLIER) cc_final: 0.6781 (tp) REVERT: B 60 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7606 (m) REVERT: B 101 TRP cc_start: 0.7699 (m-90) cc_final: 0.7311 (m-90) REVERT: B 265 TYR cc_start: 0.7139 (m-80) cc_final: 0.6631 (m-80) REVERT: B 410 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8552 (tt0) REVERT: B 467 GLU cc_start: 0.8949 (tp30) cc_final: 0.8348 (pp20) REVERT: C 265 TYR cc_start: 0.8148 (m-80) cc_final: 0.7301 (m-80) REVERT: D 46 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8659 (mm-30) REVERT: E 22 CYS cc_start: -0.0890 (OUTLIER) cc_final: -0.2168 (t) REVERT: E 82 MET cc_start: -0.5712 (tpp) cc_final: -0.5935 (ttt) REVERT: L 3 GLN cc_start: 0.7907 (mp10) cc_final: 0.7274 (mp10) REVERT: L 75 LYS cc_start: 0.9203 (mmmt) cc_final: 0.8947 (mmmm) REVERT: L 107 GLN cc_start: 0.8028 (mp10) cc_final: 0.7456 (mp10) outliers start: 40 outliers final: 29 residues processed: 115 average time/residue: 0.2163 time to fit residues: 38.5263 Evaluate side-chains 104 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 71 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 95 CYS Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 111 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 19 optimal weight: 0.2980 chunk 5 optimal weight: 0.0980 chunk 153 optimal weight: 10.0000 chunk 138 optimal weight: 50.0000 chunk 55 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 143 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** 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 = 0.4469 r_free = 0.4469 target = 0.162316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.112122 restraints weight = 36272.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.108630 restraints weight = 20365.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.109457 restraints weight = 17226.671| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13365 Z= 0.116 Angle : 0.551 6.932 18175 Z= 0.288 Chirality : 0.045 0.181 1987 Planarity : 0.004 0.047 2326 Dihedral : 3.952 19.031 1774 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.84 % Favored : 93.97 % Rotamer: Outliers : 2.99 % Allowed : 20.32 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.98 (0.21), residues: 1592 helix: -1.46 (0.47), residues: 112 sheet: 0.79 (0.24), residues: 505 loop : -1.41 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 101 HIS 0.002 0.000 HIS A 203 PHE 0.028 0.001 PHE A 234 TYR 0.017 0.001 TYR A 156 ARG 0.002 0.000 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.02917 ( 381) hydrogen bonds : angle 5.58593 ( 963) SS BOND : bond 0.00245 ( 20) SS BOND : angle 0.89256 ( 40) covalent geometry : bond 0.00272 (13345) covalent geometry : angle 0.55041 (18135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 81 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.7124 (OUTLIER) cc_final: 0.6727 (tp) REVERT: B 60 THR cc_start: 0.8045 (OUTLIER) cc_final: 0.7726 (m) REVERT: B 93 GLU cc_start: 0.6972 (pm20) cc_final: 0.6771 (pp20) REVERT: B 101 TRP cc_start: 0.7612 (m-90) cc_final: 0.7216 (m-90) REVERT: B 265 TYR cc_start: 0.7027 (m-80) cc_final: 0.6591 (m-80) REVERT: B 410 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.7876 (tt0) REVERT: C 30 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8521 (t) REVERT: C 265 TYR cc_start: 0.8206 (m-80) cc_final: 0.7423 (m-80) REVERT: D 3 GLN cc_start: 0.8795 (mm110) cc_final: 0.8494 (mm-40) REVERT: E 22 CYS cc_start: -0.1112 (OUTLIER) cc_final: -0.2120 (t) REVERT: L 107 GLN cc_start: 0.8030 (mp10) cc_final: 0.7718 (mp10) outliers start: 43 outliers final: 27 residues processed: 118 average time/residue: 0.2249 time to fit residues: 41.0553 Evaluate side-chains 102 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 95 CYS Chi-restraints excluded: chain L residue 102 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 63 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 16 optimal weight: 0.0270 chunk 66 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 ASN D 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.161768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.110650 restraints weight = 35726.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.106785 restraints weight = 19129.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.107894 restraints weight = 16636.345| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13365 Z= 0.200 Angle : 0.611 6.938 18175 Z= 0.323 Chirality : 0.046 0.178 1987 Planarity : 0.005 0.090 2326 Dihedral : 4.307 20.442 1774 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.34 % Favored : 93.47 % Rotamer: Outliers : 3.27 % Allowed : 20.74 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.21 (0.21), residues: 1592 helix: -1.53 (0.46), residues: 116 sheet: 0.56 (0.24), residues: 486 loop : -1.50 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 432 HIS 0.003 0.001 HIS C 203 PHE 0.031 0.002 PHE A 234 TYR 0.018 0.001 TYR D 94 ARG 0.008 0.001 ARG D 45 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 381) hydrogen bonds : angle 5.79497 ( 963) SS BOND : bond 0.00388 ( 20) SS BOND : angle 1.30325 ( 40) covalent geometry : bond 0.00469 (13345) covalent geometry : angle 0.60823 (18135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 72 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.7152 (OUTLIER) cc_final: 0.6709 (tp) REVERT: B 265 TYR cc_start: 0.7073 (m-80) cc_final: 0.6582 (m-80) REVERT: B 410 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8653 (mt0) REVERT: B 467 GLU cc_start: 0.8726 (tp30) cc_final: 0.8350 (pp20) REVERT: B 489 GLN cc_start: 0.8332 (mt0) cc_final: 0.8119 (mt0) REVERT: C 30 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8594 (t) REVERT: D 3 GLN cc_start: 0.8892 (mm110) cc_final: 0.8635 (mm110) REVERT: D 46 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8625 (mm-30) REVERT: E 22 CYS cc_start: -0.0826 (OUTLIER) cc_final: -0.1602 (t) outliers start: 47 outliers final: 34 residues processed: 112 average time/residue: 0.2263 time to fit residues: 39.2143 Evaluate side-chains 102 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 64 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 95 CYS Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 111 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 105 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 111 optimal weight: 30.0000 chunk 76 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN A 501 HIS ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** 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 = 0.4459 r_free = 0.4459 target = 0.165692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.113611 restraints weight = 34206.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.108813 restraints weight = 21340.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.109907 restraints weight = 17850.830| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13365 Z= 0.161 Angle : 0.584 7.176 18175 Z= 0.307 Chirality : 0.046 0.255 1987 Planarity : 0.004 0.045 2326 Dihedral : 4.130 17.778 1774 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.65 % Favored : 94.16 % Rotamer: Outliers : 3.27 % Allowed : 20.81 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.11 (0.21), residues: 1592 helix: -1.50 (0.46), residues: 117 sheet: 0.64 (0.24), residues: 518 loop : -1.50 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 101 HIS 0.002 0.000 HIS C 203 PHE 0.032 0.001 PHE A 234 TYR 0.015 0.001 TYR B 485 ARG 0.004 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.03096 ( 381) hydrogen bonds : angle 5.65361 ( 963) SS BOND : bond 0.00339 ( 20) SS BOND : angle 1.12913 ( 40) covalent geometry : bond 0.00377 (13345) covalent geometry : angle 0.58213 (18135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 72 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.7210 (OUTLIER) cc_final: 0.6806 (tp) REVERT: B 101 TRP cc_start: 0.7746 (m-90) cc_final: 0.7528 (m-90) REVERT: B 173 MET cc_start: 0.7593 (pmm) cc_final: 0.7150 (ppp) REVERT: B 265 TYR cc_start: 0.7079 (m-80) cc_final: 0.6661 (m-80) REVERT: B 410 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8596 (tt0) REVERT: B 467 GLU cc_start: 0.8854 (tp30) cc_final: 0.8228 (pp20) REVERT: B 489 GLN cc_start: 0.8320 (mt0) cc_final: 0.8070 (mt0) REVERT: C 30 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8543 (t) REVERT: C 265 TYR cc_start: 0.8219 (m-80) cc_final: 0.7307 (m-80) REVERT: D 45 ARG cc_start: 0.6533 (mmm160) cc_final: 0.5797 (mmm160) outliers start: 47 outliers final: 36 residues processed: 110 average time/residue: 0.2421 time to fit residues: 40.3036 Evaluate side-chains 107 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 68 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 95 CYS Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 111 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 51 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 122 optimal weight: 0.0980 chunk 80 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 108 optimal weight: 0.3980 chunk 123 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.157406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.104324 restraints weight = 36352.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.103780 restraints weight = 19553.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.103492 restraints weight = 15164.699| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13365 Z= 0.111 Angle : 0.571 8.620 18175 Z= 0.298 Chirality : 0.045 0.232 1987 Planarity : 0.004 0.046 2326 Dihedral : 3.939 17.167 1774 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.53 % Favored : 94.28 % Rotamer: Outliers : 2.85 % Allowed : 21.02 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.21), residues: 1592 helix: -1.37 (0.50), residues: 106 sheet: 0.83 (0.24), residues: 505 loop : -1.36 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 101 HIS 0.002 0.000 HIS A 203 PHE 0.027 0.001 PHE A 234 TYR 0.015 0.001 TYR B 485 ARG 0.008 0.000 ARG B 210 Details of bonding type rmsd hydrogen bonds : bond 0.02835 ( 381) hydrogen bonds : angle 5.50465 ( 963) SS BOND : bond 0.00298 ( 20) SS BOND : angle 1.06314 ( 40) covalent geometry : bond 0.00259 (13345) covalent geometry : angle 0.56932 (18135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 75 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.7262 (OUTLIER) cc_final: 0.6827 (tp) REVERT: B 173 MET cc_start: 0.7739 (pmm) cc_final: 0.6925 (ppp) REVERT: B 265 TYR cc_start: 0.6987 (m-80) cc_final: 0.6629 (m-80) REVERT: B 410 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8490 (mt0) REVERT: B 467 GLU cc_start: 0.8818 (tp30) cc_final: 0.8310 (pp20) REVERT: B 489 GLN cc_start: 0.8240 (mt0) cc_final: 0.7983 (mt0) REVERT: C 30 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8520 (t) REVERT: C 265 TYR cc_start: 0.8244 (m-80) cc_final: 0.7475 (m-80) REVERT: E 22 CYS cc_start: -0.0600 (OUTLIER) cc_final: -0.1247 (t) REVERT: L 107 GLN cc_start: 0.8072 (mp10) cc_final: 0.7783 (mp10) outliers start: 41 outliers final: 33 residues processed: 107 average time/residue: 0.2309 time to fit residues: 37.9751 Evaluate side-chains 110 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 73 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 95 CYS Chi-restraints excluded: chain L residue 102 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 118 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 142 optimal weight: 30.0000 chunk 39 optimal weight: 0.9990 chunk 63 optimal weight: 0.0670 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 104 optimal weight: 7.9990 chunk 84 optimal weight: 0.4980 chunk 76 optimal weight: 0.5980 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** 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 = 0.4480 r_free = 0.4480 target = 0.168782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.115004 restraints weight = 34330.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.112934 restraints weight = 21083.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.112397 restraints weight = 19699.319| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13365 Z= 0.109 Angle : 0.572 8.599 18175 Z= 0.296 Chirality : 0.045 0.217 1987 Planarity : 0.004 0.113 2326 Dihedral : 3.848 16.828 1774 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.03 % Favored : 94.79 % Rotamer: Outliers : 2.71 % Allowed : 21.22 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.82 (0.21), residues: 1592 helix: -1.37 (0.50), residues: 106 sheet: 0.87 (0.24), residues: 506 loop : -1.29 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 101 HIS 0.002 0.000 HIS A 203 PHE 0.026 0.001 PHE A 234 TYR 0.017 0.001 TYR D 94 ARG 0.011 0.000 ARG D 45 Details of bonding type rmsd hydrogen bonds : bond 0.02773 ( 381) hydrogen bonds : angle 5.42424 ( 963) SS BOND : bond 0.00312 ( 20) SS BOND : angle 1.07711 ( 40) covalent geometry : bond 0.00254 (13345) covalent geometry : angle 0.57030 (18135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 74 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.7164 (OUTLIER) cc_final: 0.6732 (tp) REVERT: B 173 MET cc_start: 0.7658 (pmm) cc_final: 0.6700 (ppp) REVERT: B 265 TYR cc_start: 0.6988 (m-80) cc_final: 0.6634 (m-80) REVERT: B 410 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: B 452 PHE cc_start: 0.8840 (m-10) cc_final: 0.8634 (m-10) REVERT: B 489 GLN cc_start: 0.8225 (mt0) cc_final: 0.7970 (mt0) REVERT: C 30 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8543 (t) REVERT: C 265 TYR cc_start: 0.8209 (m-80) cc_final: 0.7492 (m-80) REVERT: D 46 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8298 (mp0) REVERT: E 22 CYS cc_start: -0.0394 (OUTLIER) cc_final: -0.1121 (t) REVERT: L 3 GLN cc_start: 0.7862 (mp10) cc_final: 0.7505 (mp10) REVERT: L 107 GLN cc_start: 0.8091 (mp10) cc_final: 0.7790 (mp10) outliers start: 39 outliers final: 34 residues processed: 104 average time/residue: 0.2525 time to fit residues: 40.3462 Evaluate side-chains 108 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 70 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 95 CYS Chi-restraints excluded: chain L residue 102 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 117 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 123 optimal weight: 30.0000 chunk 135 optimal weight: 9.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** 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 = 0.4468 r_free = 0.4468 target = 0.165801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.111484 restraints weight = 34589.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.111544 restraints weight = 19334.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.111865 restraints weight = 13641.524| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13365 Z= 0.145 Angle : 0.585 8.599 18175 Z= 0.304 Chirality : 0.045 0.217 1987 Planarity : 0.004 0.094 2326 Dihedral : 3.925 16.305 1774 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.84 % Favored : 93.97 % Rotamer: Outliers : 2.78 % Allowed : 21.22 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.93 (0.21), residues: 1592 helix: -1.47 (0.48), residues: 112 sheet: 0.82 (0.24), residues: 502 loop : -1.36 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 101 HIS 0.002 0.000 HIS A 203 PHE 0.028 0.001 PHE A 234 TYR 0.013 0.001 TYR B 485 ARG 0.012 0.000 ARG D 45 Details of bonding type rmsd hydrogen bonds : bond 0.03004 ( 381) hydrogen bonds : angle 5.49610 ( 963) SS BOND : bond 0.00295 ( 20) SS BOND : angle 1.04073 ( 40) covalent geometry : bond 0.00341 (13345) covalent geometry : angle 0.58324 (18135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4599.27 seconds wall clock time: 81 minutes 21.18 seconds (4881.18 seconds total)