Starting phenix.real_space_refine on Sun Jan 19 19:13:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9atp_43832/01_2025/9atp_43832.cif Found real_map, /net/cci-nas-00/data/ceres_data/9atp_43832/01_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_43832/01_2025/9atp_43832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9atp_43832/01_2025/9atp_43832.map" model { file = "/net/cci-nas-00/data/ceres_data/9atp_43832/01_2025/9atp_43832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9atp_43832/01_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 8.75, per 1000 atoms: 0.67 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: 2.82 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: 1.27 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: 3.56 Time building geometry restraints manager: 3.40 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: 5.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 30.850 Find NCS groups from input model: 0.640 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.670 ------------------------------------------------------------------------------- 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 13345 Z= 0.314 Angle : 0.730 11.381 18135 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 *********************** 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 : 1.405 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: 0.2617 time to fit residues: 38.5111 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 : 1.595 ------------------------------------------------------------------------------- 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: 2.9990 chunk 41 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 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: 1.5624 ------------------------------------------------------------------------------- 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 = 0.157756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.103615 restraints weight = 36154.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.102867 restraints weight = 22838.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.103412 restraints weight = 16873.687| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13345 Z= 0.271 Angle : 0.617 6.900 18135 Z= 0.330 Chirality : 0.047 0.217 1987 Planarity : 0.005 0.059 2326 Dihedral : 4.569 33.969 1780 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.28 % Favored : 93.47 % Rotamer: Outliers : 2.23 % Allowed : 19.14 % Favored : 78.64 % 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 : -1.59 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 101 HIS 0.006 0.001 HIS A 501 PHE 0.017 0.002 PHE L 67 TYR 0.014 0.001 TYR B 417 ARG 0.006 0.001 ARG D 45 *********************** 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 119 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.7014 (OUTLIER) cc_final: 0.6777 (tp) REVERT: B 101 TRP cc_start: 0.7614 (m-90) cc_final: 0.7361 (m-90) REVERT: B 467 GLU cc_start: 0.8876 (tp30) cc_final: 0.8312 (pp20) REVERT: B 515 HIS cc_start: 0.5938 (t-90) cc_final: 0.5729 (t-90) REVERT: D 46 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8137 (mm-30) REVERT: D 98 VAL cc_start: 0.6223 (t) cc_final: 0.5766 (p) REVERT: L 75 LYS cc_start: 0.9229 (mmmt) cc_final: 0.8936 (mmmm) outliers start: 32 outliers final: 17 residues processed: 111 average time/residue: 0.2506 time to fit residues: 41.8989 Evaluate side-chains 96 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 1.348 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 138 optimal weight: 50.0000 chunk 142 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 80 optimal weight: 0.0870 chunk 47 optimal weight: 0.9980 chunk 115 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 HIS ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 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 = 0.4483 r_free = 0.4483 target = 0.167181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.112918 restraints weight = 35367.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.113400 restraints weight = 20278.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.112704 restraints weight = 15371.096| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13345 Z= 0.223 Angle : 0.576 6.939 18135 Z= 0.306 Chirality : 0.046 0.192 1987 Planarity : 0.004 0.049 2326 Dihedral : 4.240 21.735 1774 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.46 % Favored : 94.28 % Rotamer: Outliers : 2.09 % Allowed : 19.69 % Favored : 78.22 % 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: -1.16 (0.21), residues: 1592 helix: -1.70 (0.45), residues: 117 sheet: 0.64 (0.23), residues: 523 loop : -1.54 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 101 HIS 0.002 0.000 HIS A 203 PHE 0.014 0.001 PHE A 234 TYR 0.011 0.001 TYR B 275 ARG 0.004 0.000 ARG D 19 *********************** 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 114 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 PHE cc_start: 0.8803 (m-80) cc_final: 0.8598 (m-80) REVERT: A 430 ILE cc_start: 0.6995 (OUTLIER) cc_final: 0.6728 (tp) REVERT: B 101 TRP cc_start: 0.7612 (m-90) cc_final: 0.7306 (m-90) REVERT: B 467 GLU cc_start: 0.8906 (tp30) cc_final: 0.8332 (pp20) REVERT: L 75 LYS cc_start: 0.9240 (mmmt) cc_final: 0.8933 (mmmm) REVERT: L 107 GLN cc_start: 0.7944 (mp10) cc_final: 0.7618 (mp10) outliers start: 30 outliers final: 19 residues processed: 107 average time/residue: 0.2407 time to fit residues: 38.9783 Evaluate side-chains 96 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 1.475 ------------------------------------------------------------------------------- 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 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 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 B residue 423 ASP 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 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: 1.9990 chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 148 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 152 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN L 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.156209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.102279 restraints weight = 36204.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.102673 restraints weight = 19424.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.102035 restraints weight = 14880.912| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13345 Z= 0.296 Angle : 0.601 7.122 18135 Z= 0.318 Chirality : 0.046 0.189 1987 Planarity : 0.004 0.048 2326 Dihedral : 4.350 18.015 1774 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.53 % Favored : 93.22 % Rotamer: Outliers : 3.34 % Allowed : 19.62 % Favored : 77.04 % 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: -1.24 (0.21), residues: 1592 helix: -1.70 (0.45), residues: 117 sheet: 0.53 (0.23), residues: 525 loop : -1.58 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 101 HIS 0.003 0.001 HIS A 501 PHE 0.015 0.002 PHE A 130 TYR 0.019 0.001 TYR A 156 ARG 0.007 0.000 ARG D 38 *********************** 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 126 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 78 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 PHE cc_start: 0.9065 (m-80) cc_final: 0.8860 (m-80) REVERT: A 430 ILE cc_start: 0.7063 (OUTLIER) cc_final: 0.6734 (tp) REVERT: B 60 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7754 (m) REVERT: B 101 TRP cc_start: 0.7708 (m-90) cc_final: 0.7326 (m-90) REVERT: B 211 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8340 (m-30) REVERT: B 410 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8627 (mt0) REVERT: B 467 GLU cc_start: 0.8911 (tp30) cc_final: 0.8300 (pp20) REVERT: B 515 HIS cc_start: 0.6145 (t-90) cc_final: 0.5935 (t-90) REVERT: L 75 LYS cc_start: 0.9237 (mmmt) cc_final: 0.8999 (mmmm) outliers start: 48 outliers final: 29 residues processed: 121 average time/residue: 0.2257 time to fit residues: 41.6584 Evaluate side-chains 102 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 111 THR 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 39 VAL 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 163 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 211 ASP 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 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 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 L residue 57 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 4 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 123 optimal weight: 20.0000 chunk 35 optimal weight: 8.9990 chunk 80 optimal weight: 0.6980 chunk 41 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 126 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 136 optimal weight: 30.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 446 ASN D 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.154677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.099250 restraints weight = 36237.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.099349 restraints weight = 21015.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.099279 restraints weight = 15669.741| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 13345 Z= 0.365 Angle : 0.630 6.960 18135 Z= 0.334 Chirality : 0.047 0.198 1987 Planarity : 0.005 0.050 2326 Dihedral : 4.605 20.250 1774 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.72 % Favored : 93.03 % Rotamer: Outliers : 3.69 % Allowed : 20.39 % 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: -1.40 (0.20), residues: 1592 helix: -1.68 (0.45), residues: 116 sheet: 0.40 (0.24), residues: 490 loop : -1.62 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 61 HIS 0.004 0.001 HIS C 203 PHE 0.018 0.002 PHE B 89 TYR 0.023 0.002 TYR D 94 ARG 0.008 0.000 ARG B 210 *********************** 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 126 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 73 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 PHE cc_start: 0.9190 (m-80) cc_final: 0.8987 (m-80) REVERT: A 430 ILE cc_start: 0.7325 (OUTLIER) cc_final: 0.6833 (tp) REVERT: B 60 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7875 (m) REVERT: B 265 TYR cc_start: 0.7219 (m-80) cc_final: 0.6676 (m-80) REVERT: B 410 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8702 (mt0) REVERT: B 467 GLU cc_start: 0.8922 (tp30) cc_final: 0.8281 (pp20) REVERT: D 3 GLN cc_start: 0.8883 (mm110) cc_final: 0.8605 (mm-40) REVERT: E 22 CYS cc_start: -0.0666 (OUTLIER) cc_final: -0.2346 (t) REVERT: E 82 MET cc_start: -0.5464 (tpp) cc_final: -0.5702 (ttt) REVERT: L 3 GLN cc_start: 0.7705 (mp10) cc_final: 0.6947 (mp10) outliers start: 53 outliers final: 36 residues processed: 120 average time/residue: 0.2306 time to fit residues: 42.8488 Evaluate side-chains 108 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 68 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 111 THR 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 204 THR 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 60 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 206 ILE 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 B residue 485 TYR 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 220 GLU 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: 0.9990 chunk 5 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 138 optimal weight: 30.0000 chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 117 optimal weight: 0.0670 chunk 67 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 143 optimal weight: 50.0000 chunk 96 optimal weight: 5.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- 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 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 HIS D 32 ASN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.166658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.114870 restraints weight = 34571.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.110328 restraints weight = 20576.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.110884 restraints weight = 17474.069| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13345 Z= 0.170 Angle : 0.560 6.926 18135 Z= 0.295 Chirality : 0.045 0.181 1987 Planarity : 0.004 0.046 2326 Dihedral : 4.069 19.760 1774 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.72 % Favored : 94.10 % Rotamer: Outliers : 3.34 % Allowed : 20.46 % Favored : 76.20 % 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: -1.15 (0.21), residues: 1592 helix: -1.56 (0.45), residues: 117 sheet: 0.72 (0.24), residues: 497 loop : -1.55 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 101 HIS 0.002 0.000 HIS A 501 PHE 0.015 0.001 PHE A 234 TYR 0.019 0.001 TYR D 94 ARG 0.004 0.000 ARG D 19 *********************** 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 125 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 77 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.8996 (p90) REVERT: A 334 PHE cc_start: 0.9245 (m-80) cc_final: 0.9022 (m-80) REVERT: A 430 ILE cc_start: 0.7172 (OUTLIER) cc_final: 0.6769 (tp) REVERT: B 60 THR cc_start: 0.8175 (OUTLIER) cc_final: 0.7908 (m) REVERT: B 101 TRP cc_start: 0.7635 (m-90) cc_final: 0.7278 (m-90) REVERT: B 265 TYR cc_start: 0.7081 (m-80) cc_final: 0.6637 (m-80) REVERT: B 410 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8666 (mt0) REVERT: B 467 GLU cc_start: 0.8970 (tp30) cc_final: 0.8382 (pp20) REVERT: C 30 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.8509 (t) REVERT: C 265 TYR cc_start: 0.8201 (m-80) cc_final: 0.7358 (m-80) REVERT: D 3 GLN cc_start: 0.8864 (mm110) cc_final: 0.8638 (mm-40) REVERT: E 22 CYS cc_start: -0.0814 (OUTLIER) cc_final: -0.1734 (t) REVERT: E 82 MET cc_start: -0.5226 (tpp) cc_final: -0.5478 (ttt) REVERT: L 107 GLN cc_start: 0.8021 (mp10) cc_final: 0.7748 (mp10) outliers start: 48 outliers final: 28 residues processed: 120 average time/residue: 0.2534 time to fit residues: 44.9558 Evaluate side-chains 100 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 66 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 111 THR 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 234 PHE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 206 ILE 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 347 TYR 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 79 HIS 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 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: 5.9990 chunk 15 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4434 r_free = 0.4434 target = 0.155868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.101055 restraints weight = 36377.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.101221 restraints weight = 20977.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.101109 restraints weight = 14376.375| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13345 Z= 0.241 Angle : 0.585 6.905 18135 Z= 0.308 Chirality : 0.046 0.248 1987 Planarity : 0.004 0.046 2326 Dihedral : 4.160 19.429 1774 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.84 % Favored : 93.97 % Rotamer: Outliers : 3.20 % Allowed : 20.81 % 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: -1.19 (0.21), residues: 1592 helix: -1.64 (0.44), residues: 123 sheet: 0.69 (0.24), residues: 504 loop : -1.57 (0.19), residues: 965 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 0.014 0.001 PHE A 234 TYR 0.017 0.001 TYR D 94 ARG 0.008 0.000 ARG L 19 *********************** 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 116 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 70 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.7362 (OUTLIER) cc_final: 0.6880 (tp) REVERT: B 60 THR cc_start: 0.8185 (OUTLIER) cc_final: 0.7974 (m) REVERT: B 265 TYR cc_start: 0.7062 (m-80) cc_final: 0.6630 (m-80) REVERT: B 410 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8578 (tt0) REVERT: C 30 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8578 (t) REVERT: D 3 GLN cc_start: 0.8944 (mm110) cc_final: 0.8717 (mm110) REVERT: E 22 CYS cc_start: -0.0427 (OUTLIER) cc_final: -0.1419 (t) REVERT: L 1 GLN cc_start: 0.8030 (tp40) cc_final: 0.7517 (tp-100) REVERT: L 107 GLN cc_start: 0.8011 (mp10) cc_final: 0.7712 (mp10) outliers start: 46 outliers final: 31 residues processed: 109 average time/residue: 0.2421 time to fit residues: 40.6944 Evaluate side-chains 99 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 63 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 111 THR 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 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 60 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 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 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 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: 0.6980 chunk 58 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 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: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN ** L 3 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 = 0.4423 r_free = 0.4423 target = 0.160443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.110457 restraints weight = 35344.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.104816 restraints weight = 18821.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.106693 restraints weight = 16308.480| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 13345 Z= 0.365 Angle : 0.643 7.326 18135 Z= 0.342 Chirality : 0.047 0.230 1987 Planarity : 0.004 0.046 2326 Dihedral : 4.487 19.264 1774 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.97 % Favored : 92.78 % Rotamer: Outliers : 3.55 % Allowed : 21.16 % Favored : 75.30 % 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: -1.37 (0.21), residues: 1592 helix: -1.68 (0.43), residues: 128 sheet: 0.40 (0.24), residues: 495 loop : -1.58 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 101 HIS 0.004 0.001 HIS C 203 PHE 0.033 0.002 PHE A 234 TYR 0.019 0.002 TYR B 166 ARG 0.008 0.001 ARG L 19 *********************** 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 122 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 71 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7081 (tp) REVERT: B 265 TYR cc_start: 0.6993 (m-80) cc_final: 0.6567 (m-80) REVERT: B 410 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8631 (mt0) REVERT: B 467 GLU cc_start: 0.8708 (tp30) cc_final: 0.8222 (pp20) REVERT: C 30 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8579 (t) REVERT: D 3 GLN cc_start: 0.8985 (mm110) cc_final: 0.8737 (mm110) REVERT: E 22 CYS cc_start: -0.0464 (OUTLIER) cc_final: -0.1207 (t) REVERT: L 1 GLN cc_start: 0.8037 (tp40) cc_final: 0.7628 (tp-100) REVERT: L 75 LYS cc_start: 0.9177 (mmmm) cc_final: 0.8975 (mmmm) REVERT: L 107 GLN cc_start: 0.7978 (mp10) cc_final: 0.7481 (mp10) outliers start: 51 outliers final: 40 residues processed: 115 average time/residue: 0.2341 time to fit residues: 41.3418 Evaluate side-chains 109 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 65 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 111 THR 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 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 97 ILE Chi-restraints excluded: chain B residue 102 ILE 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 345 SER 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 204 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 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 27 SER 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: 4.9990 chunk 19 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 122 optimal weight: 20.0000 chunk 80 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 108 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 7 optimal weight: 0.0370 chunk 9 optimal weight: 0.2980 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.157678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.103236 restraints weight = 35481.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.103279 restraints weight = 19466.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.102937 restraints weight = 14422.698| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13345 Z= 0.161 Angle : 0.572 8.733 18135 Z= 0.301 Chirality : 0.045 0.192 1987 Planarity : 0.004 0.044 2326 Dihedral : 4.031 18.660 1774 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.59 % Favored : 94.22 % Rotamer: Outliers : 2.30 % Allowed : 22.13 % Favored : 75.57 % 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: -1.10 (0.21), residues: 1592 helix: -1.51 (0.46), residues: 117 sheet: 0.74 (0.24), residues: 497 loop : -1.50 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 101 HIS 0.002 0.000 HIS B 63 PHE 0.028 0.001 PHE A 234 TYR 0.021 0.001 TYR D 94 ARG 0.007 0.000 ARG L 19 *********************** 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 104 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 71 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7035 (tp) REVERT: B 265 TYR cc_start: 0.6812 (m-80) cc_final: 0.6546 (m-80) REVERT: B 410 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8572 (tt0) REVERT: C 30 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8503 (t) REVERT: C 265 TYR cc_start: 0.8160 (m-80) cc_final: 0.7388 (m-80) REVERT: D 3 GLN cc_start: 0.8980 (mm110) cc_final: 0.8745 (mm110) REVERT: D 45 ARG cc_start: 0.6658 (mmm-85) cc_final: 0.6321 (mmm-85) REVERT: D 46 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8663 (mm-30) REVERT: L 1 GLN cc_start: 0.8039 (tp40) cc_final: 0.7611 (tp-100) REVERT: L 107 GLN cc_start: 0.8014 (mp10) cc_final: 0.7730 (mp10) outliers start: 33 outliers final: 28 residues processed: 97 average time/residue: 0.2560 time to fit residues: 36.6410 Evaluate side-chains 98 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 111 THR 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 337 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 97 ILE Chi-restraints excluded: chain B residue 163 THR 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 410 GLN 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 118 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 63 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** 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 = 0.4454 r_free = 0.4454 target = 0.164825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.110108 restraints weight = 34629.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.109977 restraints weight = 20122.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.110711 restraints weight = 15039.760| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13345 Z= 0.215 Angle : 0.582 8.932 18135 Z= 0.306 Chirality : 0.045 0.196 1987 Planarity : 0.004 0.044 2326 Dihedral : 4.005 18.341 1774 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.90 % Favored : 93.91 % Rotamer: Outliers : 2.57 % Allowed : 21.92 % Favored : 75.50 % 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: -1.08 (0.21), residues: 1592 helix: -1.51 (0.46), residues: 117 sheet: 0.71 (0.24), residues: 508 loop : -1.48 (0.19), residues: 967 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 0.030 0.001 PHE A 234 TYR 0.016 0.001 TYR B 485 ARG 0.007 0.000 ARG L 19 ********************** 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 105 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 68 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASN cc_start: 0.8012 (t0) cc_final: 0.7687 (p0) REVERT: A 430 ILE cc_start: 0.7496 (OUTLIER) cc_final: 0.7026 (tp) REVERT: B 173 MET cc_start: 0.7665 (pmm) cc_final: 0.6963 (ppp) REVERT: B 265 TYR cc_start: 0.7078 (m-80) cc_final: 0.6708 (m-80) REVERT: C 30 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8536 (t) REVERT: D 3 GLN cc_start: 0.8957 (mm110) cc_final: 0.8712 (mm110) REVERT: D 45 ARG cc_start: 0.6741 (mmm-85) cc_final: 0.6399 (mmm-85) REVERT: D 46 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8587 (mm-30) REVERT: E 22 CYS cc_start: -0.0663 (OUTLIER) cc_final: -0.1436 (t) REVERT: L 1 GLN cc_start: 0.7944 (tp40) cc_final: 0.7548 (tp-100) REVERT: L 107 GLN cc_start: 0.7992 (mp10) cc_final: 0.7689 (mp10) outliers start: 37 outliers final: 30 residues processed: 98 average time/residue: 0.2461 time to fit residues: 36.3942 Evaluate side-chains 99 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 66 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 111 THR 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 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 97 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 455 SER 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 204 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 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 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: 0.0270 chunk 39 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 140 optimal weight: 30.0000 chunk 21 optimal weight: 0.9990 chunk 123 optimal weight: 8.9990 chunk 135 optimal weight: 8.9990 overall best weight: 0.7442 ------------------------------------------------------------------------------- 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 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 = 0.4460 r_free = 0.4460 target = 0.165044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.110462 restraints weight = 34722.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.111330 restraints weight = 20296.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.111030 restraints weight = 14236.805| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13345 Z= 0.176 Angle : 0.575 8.861 18135 Z= 0.301 Chirality : 0.045 0.183 1987 Planarity : 0.004 0.044 2326 Dihedral : 3.957 18.090 1774 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.78 % Favored : 94.03 % Rotamer: Outliers : 2.51 % Allowed : 22.06 % Favored : 75.43 % 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: -1.48 (0.47), residues: 117 sheet: 0.78 (0.24), residues: 506 loop : -1.47 (0.19), residues: 969 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 0.029 0.001 PHE A 234 TYR 0.016 0.001 TYR D 94 ARG 0.007 0.000 ARG L 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4380.21 seconds wall clock time: 80 minutes 19.26 seconds (4819.26 seconds total)