Starting phenix.real_space_refine on Thu Jun 12 17:34:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9atp_43832/06_2025/9atp_43832.cif Found real_map, /net/cci-nas-00/data/ceres_data/9atp_43832/06_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_43832/06_2025/9atp_43832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9atp_43832/06_2025/9atp_43832.map" model { file = "/net/cci-nas-00/data/ceres_data/9atp_43832/06_2025/9atp_43832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9atp_43832/06_2025/9atp_43832.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1380 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 8379 2.51 5 N 2153 2.21 5 O 2420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.72, 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: 2.67 Conformation dependent library (CDL) restraints added in 1.5 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: 1.46 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: 3.75 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4093 1.34 - 1.47: 3549 1.47 - 1.59: 5642 1.59 - 1.71: 0 1.71 - 1.83: 61 Bond restraints: 13345 Sorted by residual: bond pdb=" CB ASP A 194 " pdb=" CG ASP A 194 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.37e+00 bond pdb=" CA LEU B 272 " pdb=" CB LEU B 272 " ideal model delta sigma weight residual 1.528 1.507 0.021 1.51e-02 4.39e+03 1.98e+00 bond pdb=" CA ASP A 194 " pdb=" CB ASP A 194 " ideal model delta sigma weight residual 1.529 1.551 -0.022 1.62e-02 3.81e+03 1.87e+00 bond pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " ideal model delta sigma weight residual 1.808 1.768 0.040 3.30e-02 9.18e+02 1.45e+00 bond pdb=" CD LYS L 64 " pdb=" CE LYS L 64 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.32e+00 ... (remaining 13340 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 17779 2.28 - 4.55: 313 4.55 - 6.83: 37 6.83 - 9.10: 5 9.10 - 11.38: 1 Bond angle restraints: 18135 Sorted by residual: angle pdb=" N GLY L 10 " pdb=" CA GLY L 10 " pdb=" C GLY L 10 " ideal model delta sigma weight residual 110.43 116.02 -5.59 1.35e+00 5.49e-01 1.71e+01 angle pdb=" CB MET L 82 " pdb=" CG MET L 82 " pdb=" SD MET L 82 " ideal model delta sigma weight residual 112.70 124.08 -11.38 3.00e+00 1.11e-01 1.44e+01 angle pdb=" N GLY E 10 " pdb=" CA GLY E 10 " pdb=" C GLY E 10 " ideal model delta sigma weight residual 110.43 115.44 -5.01 1.35e+00 5.49e-01 1.38e+01 angle pdb=" CA GLU A 129 " pdb=" CB GLU A 129 " pdb=" CG GLU A 129 " ideal model delta sigma weight residual 114.10 121.50 -7.40 2.00e+00 2.50e-01 1.37e+01 angle pdb=" N GLY A 100 " pdb=" CA GLY A 100 " pdb=" C GLY A 100 " ideal model delta sigma weight residual 110.56 115.28 -4.72 1.36e+00 5.41e-01 1.20e+01 ... (remaining 18130 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6867 17.95 - 35.90: 818 35.90 - 53.86: 143 53.86 - 71.81: 14 71.81 - 89.76: 12 Dihedral angle restraints: 7854 sinusoidal: 3078 harmonic: 4776 Sorted by residual: dihedral pdb=" CA LYS A 94 " pdb=" C LYS A 94 " pdb=" N SER A 95 " pdb=" CA SER A 95 " ideal model delta harmonic sigma weight residual 180.00 155.40 24.60 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CB CYS B 476 " pdb=" SG CYS B 476 " pdb=" SG CYS B 484 " pdb=" CB CYS B 484 " ideal model delta sinusoidal sigma weight residual 93.00 53.81 39.19 1 1.00e+01 1.00e-02 2.16e+01 dihedral pdb=" CA ALA B 516 " pdb=" C ALA B 516 " pdb=" N PRO B 517 " pdb=" CA PRO B 517 " ideal model delta harmonic sigma weight residual 180.00 -157.63 -22.37 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 7851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1726 0.074 - 0.148: 247 0.148 - 0.222: 10 0.222 - 0.295: 1 0.295 - 0.369: 3 Chirality restraints: 1987 Sorted by residual: chirality pdb=" CB VAL L 63 " pdb=" CA VAL L 63 " pdb=" CG1 VAL L 63 " pdb=" CG2 VAL L 63 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CB THR C 30 " pdb=" CA THR C 30 " pdb=" OG1 THR C 30 " pdb=" CG2 THR C 30 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB ILE E 28 " pdb=" CA ILE E 28 " pdb=" CG1 ILE E 28 " pdb=" CG2 ILE E 28 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 1984 not shown) Planarity restraints: 2326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 101 " 0.026 2.00e-02 2.50e+03 2.81e-02 1.97e+01 pdb=" CG TRP B 101 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP B 101 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP B 101 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 101 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 101 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 101 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 101 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 101 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 101 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 516 " -0.056 5.00e-02 4.00e+02 8.48e-02 1.15e+01 pdb=" N PRO B 517 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO B 517 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 517 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 225 " 0.039 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO C 226 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 226 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 226 " 0.032 5.00e-02 4.00e+02 ... (remaining 2323 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 186 2.61 - 3.19: 11356 3.19 - 3.76: 19072 3.76 - 4.33: 26290 4.33 - 4.90: 43357 Nonbonded interactions: 100261 Sorted by model distance: nonbonded pdb=" OD1 ASP L 99 " pdb=" N LYS L 100 " model vdw 2.043 3.120 nonbonded pdb=" NH2 ARG L 66 " pdb=" O SER L 84 " model vdw 2.133 3.120 nonbonded pdb=" NH2 ARG B 31 " pdb=" O PRO B 213 " model vdw 2.169 3.120 nonbonded pdb=" OE1 GLN C 49 " pdb=" OG1 THR C 270 " model vdw 2.177 3.040 nonbonded pdb=" OH TYR A 88 " pdb=" OE1 GLU A 187 " model vdw 2.209 3.040 ... (remaining 100256 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 62 or resid 83 through 173 or resid 184 through \ 466 or resid 486 through 525)) selection = (chain 'B' and (resid 22 through 62 or resid 83 through 173 or resid 184 through \ 466 or resid 486 through 525)) selection = (chain 'C' and (resid 22 through 62 or resid 83 through 525)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 30.550 Find NCS groups from input model: 0.540 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13365 Z= 0.216 Angle : 0.731 11.381 18175 Z= 0.396 Chirality : 0.050 0.369 1987 Planarity : 0.005 0.085 2326 Dihedral : 15.179 89.758 4726 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.22 % Favored : 93.47 % Rotamer: Outliers : 0.21 % Allowed : 21.50 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.20), residues: 1592 helix: -2.04 (0.48), residues: 103 sheet: 0.37 (0.22), residues: 540 loop : -1.64 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP B 101 HIS 0.020 0.001 HIS A 501 PHE 0.038 0.002 PHE L 67 TYR 0.016 0.002 TYR B 166 ARG 0.008 0.001 ARG B 462 Details of bonding type rmsd hydrogen bonds : bond 0.11307 ( 381) hydrogen bonds : angle 7.20549 ( 963) SS BOND : bond 0.00727 ( 20) SS BOND : angle 1.02484 ( 40) covalent geometry : bond 0.00489 (13345) covalent geometry : angle 0.73022 (18135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 1.329 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: 0.2492 time to fit residues: 36.3437 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 : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 474 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 125 optimal weight: 50.0000 chunk 48 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 145 optimal weight: 0.0170 overall best weight: 1.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.157848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.103699 restraints weight = 36174.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.103244 restraints weight = 22266.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.103569 restraints weight = 16412.929| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13365 Z= 0.181 Angle : 0.616 6.876 18175 Z= 0.330 Chirality : 0.047 0.220 1987 Planarity : 0.005 0.064 2326 Dihedral : 4.555 34.244 1780 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.28 % Favored : 93.47 % Rotamer: Outliers : 2.30 % Allowed : 18.93 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.21), residues: 1592 helix: -1.84 (0.44), residues: 117 sheet: 0.54 (0.23), residues: 529 loop : -1.58 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 101 HIS 0.007 0.001 HIS A 501 PHE 0.017 0.002 PHE L 67 TYR 0.014 0.001 TYR B 491 ARG 0.006 0.001 ARG D 45 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 381) hydrogen bonds : angle 6.23120 ( 963) SS BOND : bond 0.00287 ( 20) SS BOND : angle 0.93727 ( 40) covalent geometry : bond 0.00418 (13345) covalent geometry : angle 0.61549 (18135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.7023 (OUTLIER) cc_final: 0.6781 (tp) REVERT: B 101 TRP cc_start: 0.7604 (m-90) cc_final: 0.7386 (m-90) REVERT: B 467 GLU cc_start: 0.8857 (tp30) cc_final: 0.8312 (pp20) REVERT: D 46 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8046 (mm-30) REVERT: D 98 VAL cc_start: 0.6267 (t) cc_final: 0.5809 (p) REVERT: L 75 LYS cc_start: 0.9229 (mmmt) cc_final: 0.8938 (mmmm) outliers start: 33 outliers final: 19 residues processed: 111 average time/residue: 0.2381 time to fit residues: 39.9057 Evaluate side-chains 98 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 111 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 43 optimal weight: 6.9990 chunk 117 optimal weight: 0.0770 chunk 138 optimal weight: 50.0000 chunk 142 optimal weight: 0.0060 chunk 146 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 115 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.0158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 HIS ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** D 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.170981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.117862 restraints weight = 36265.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.117268 restraints weight = 19650.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.117173 restraints weight = 16463.581| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13365 Z= 0.135 Angle : 0.570 6.926 18175 Z= 0.302 Chirality : 0.045 0.195 1987 Planarity : 0.004 0.049 2326 Dihedral : 4.182 21.282 1774 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.53 % Favored : 94.22 % Rotamer: Outliers : 2.09 % Allowed : 19.49 % Favored : 78.43 % 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: -1.11 (0.21), residues: 1592 helix: -1.68 (0.45), residues: 117 sheet: 0.68 (0.22), residues: 541 loop : -1.56 (0.20), residues: 934 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 0.013 0.001 PHE A 234 TYR 0.010 0.001 TYR B 275 ARG 0.003 0.000 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.03282 ( 381) hydrogen bonds : angle 5.93377 ( 963) SS BOND : bond 0.00266 ( 20) SS BOND : angle 0.85377 ( 40) covalent geometry : bond 0.00313 (13345) covalent geometry : angle 0.56890 (18135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.6980 (OUTLIER) cc_final: 0.6736 (tp) REVERT: B 101 TRP cc_start: 0.7569 (m-90) cc_final: 0.7228 (m-90) REVERT: B 467 GLU cc_start: 0.8881 (tp30) cc_final: 0.8301 (pp20) REVERT: L 50 PHE cc_start: 0.8554 (m-80) cc_final: 0.8048 (m-80) REVERT: L 75 LYS cc_start: 0.9241 (mmmt) cc_final: 0.8922 (mmmm) REVERT: L 107 GLN cc_start: 0.7910 (mp10) cc_final: 0.7603 (mp10) outliers start: 30 outliers final: 17 residues processed: 111 average time/residue: 0.2359 time to fit residues: 39.9280 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 : 1.443 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 HIS B 515 HIS D 32 ASN L 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.156587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.102850 restraints weight = 36112.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.101464 restraints weight = 21731.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.102002 restraints weight = 16757.476| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13365 Z= 0.187 Angle : 0.591 6.987 18175 Z= 0.313 Chirality : 0.046 0.188 1987 Planarity : 0.004 0.048 2326 Dihedral : 4.267 17.266 1774 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.41 % Favored : 93.34 % Rotamer: Outliers : 3.06 % Allowed : 19.83 % Favored : 77.11 % 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: -1.22 (0.20), residues: 1592 helix: -1.64 (0.45), residues: 117 sheet: 0.55 (0.23), residues: 501 loop : -1.52 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 101 HIS 0.005 0.001 HIS B 515 PHE 0.015 0.002 PHE B 89 TYR 0.021 0.001 TYR A 156 ARG 0.003 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.03397 ( 381) hydrogen bonds : angle 5.91926 ( 963) SS BOND : bond 0.00301 ( 20) SS BOND : angle 0.86477 ( 40) covalent geometry : bond 0.00432 (13345) covalent geometry : angle 0.58996 (18135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 83 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.7008 (OUTLIER) cc_final: 0.6692 (tp) REVERT: B 60 THR cc_start: 0.8010 (OUTLIER) cc_final: 0.7700 (m) REVERT: B 265 TYR cc_start: 0.7048 (m-80) cc_final: 0.6546 (m-80) REVERT: B 410 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8626 (mt0) REVERT: B 467 GLU cc_start: 0.8913 (tp30) cc_final: 0.8312 (pp20) REVERT: D 46 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8566 (mm-30) REVERT: E 82 MET cc_start: -0.5766 (tpp) cc_final: -0.6007 (ttt) REVERT: L 75 LYS cc_start: 0.9214 (mmmt) cc_final: 0.8970 (mmmm) outliers start: 44 outliers final: 28 residues processed: 122 average time/residue: 0.2397 time to fit residues: 44.5237 Evaluate side-chains 101 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 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 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 30 SER 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=3.50 ------------------------------------------------------------------------------- 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: 0.0040 chunk 80 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 127 optimal weight: 30.0000 chunk 126 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- 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 446 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.168419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.113271 restraints weight = 34884.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.113936 restraints weight = 20331.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.113745 restraints weight = 14410.934| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13365 Z= 0.177 Angle : 0.585 6.997 18175 Z= 0.307 Chirality : 0.046 0.181 1987 Planarity : 0.004 0.050 2326 Dihedral : 4.255 19.350 1774 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.90 % Favored : 93.91 % Rotamer: Outliers : 3.41 % Allowed : 20.04 % Favored : 76.55 % 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: -1.48 (0.47), residues: 110 sheet: 0.64 (0.23), residues: 524 loop : -1.57 (0.19), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 101 HIS 0.003 0.001 HIS A 501 PHE 0.014 0.001 PHE B 89 TYR 0.016 0.001 TYR B 485 ARG 0.004 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.03246 ( 381) hydrogen bonds : angle 5.82041 ( 963) SS BOND : bond 0.00443 ( 20) SS BOND : angle 0.98109 ( 40) covalent geometry : bond 0.00416 (13345) covalent geometry : angle 0.58338 (18135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 76 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.7198 (OUTLIER) cc_final: 0.6789 (tp) REVERT: B 60 THR cc_start: 0.8120 (OUTLIER) cc_final: 0.7790 (m) REVERT: B 101 TRP cc_start: 0.7653 (m-90) cc_final: 0.7313 (m-90) REVERT: B 265 TYR cc_start: 0.7142 (m-80) cc_final: 0.6633 (m-80) REVERT: B 410 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8651 (mt0) REVERT: B 467 GLU cc_start: 0.8926 (tp30) cc_final: 0.8288 (pp20) REVERT: D 3 GLN cc_start: 0.8765 (mm110) cc_final: 0.8468 (mm-40) REVERT: D 46 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8590 (mm-30) REVERT: E 22 CYS cc_start: -0.0866 (OUTLIER) cc_final: -0.2370 (t) REVERT: L 3 GLN cc_start: 0.7677 (mp10) cc_final: 0.6894 (mp10) REVERT: L 75 LYS cc_start: 0.9229 (mmmt) cc_final: 0.8986 (mmmm) REVERT: L 107 GLN cc_start: 0.7960 (mp10) cc_final: 0.7431 (mp10) outliers start: 49 outliers final: 37 residues processed: 119 average time/residue: 0.2194 time to fit residues: 40.8531 Evaluate side-chains 111 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 70 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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 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 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 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 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 E residue 22 CYS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 57 THR 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: 0.0060 chunk 5 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 138 optimal weight: 30.0000 chunk 55 optimal weight: 0.5980 chunk 78 optimal weight: 0.1980 chunk 117 optimal weight: 50.0000 chunk 67 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 ** 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 = 0.4476 r_free = 0.4476 target = 0.163014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.112942 restraints weight = 36176.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.109320 restraints weight = 19924.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.109586 restraints weight = 16985.071| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13365 Z= 0.102 Angle : 0.541 6.932 18175 Z= 0.283 Chirality : 0.045 0.181 1987 Planarity : 0.004 0.048 2326 Dihedral : 3.872 19.385 1774 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.59 % Favored : 94.22 % Rotamer: Outliers : 3.20 % Allowed : 20.18 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.21), residues: 1592 helix: -1.41 (0.47), residues: 112 sheet: 0.85 (0.24), residues: 503 loop : -1.44 (0.19), residues: 977 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 B 485 ARG 0.003 0.000 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.02801 ( 381) hydrogen bonds : angle 5.53658 ( 963) SS BOND : bond 0.00250 ( 20) SS BOND : angle 0.92143 ( 40) covalent geometry : bond 0.00235 (13345) covalent geometry : angle 0.54014 (18135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 83 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.7100 (OUTLIER) cc_final: 0.6691 (tp) REVERT: B 60 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7791 (m) REVERT: B 101 TRP cc_start: 0.7523 (m-90) cc_final: 0.7179 (m-90) REVERT: B 265 TYR cc_start: 0.7009 (m-80) cc_final: 0.6623 (m-80) REVERT: B 410 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.7865 (tt0) REVERT: B 467 GLU cc_start: 0.8890 (tp30) cc_final: 0.8442 (pp20) REVERT: C 30 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8495 (t) REVERT: C 265 TYR cc_start: 0.8211 (m-80) cc_final: 0.7445 (m-80) REVERT: D 3 GLN cc_start: 0.8862 (mm110) cc_final: 0.8567 (mm-40) REVERT: E 22 CYS cc_start: -0.0947 (OUTLIER) cc_final: -0.1917 (t) REVERT: L 88 GLU cc_start: 0.9182 (pm20) cc_final: 0.8980 (pm20) REVERT: L 107 GLN cc_start: 0.8049 (mp10) cc_final: 0.7771 (mp10) outliers start: 46 outliers final: 28 residues processed: 123 average time/residue: 0.2338 time to fit residues: 44.6024 Evaluate side-chains 103 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 70 time to evaluate : 1.567 ------------------------------------------------------------------------------- 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 132 PHE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 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 485 TYR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 98 ILE 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 30 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 113 VAL 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: 3.9990 chunk 26 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.160516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.110715 restraints weight = 35521.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.105156 restraints weight = 19959.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.105934 restraints weight = 16500.820| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13365 Z= 0.272 Angle : 0.664 7.460 18175 Z= 0.353 Chirality : 0.048 0.259 1987 Planarity : 0.005 0.047 2326 Dihedral : 4.612 19.112 1774 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.91 % Favored : 92.84 % Rotamer: Outliers : 3.76 % Allowed : 20.25 % 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: -1.36 (0.20), residues: 1592 helix: -1.64 (0.44), residues: 122 sheet: 0.39 (0.24), residues: 505 loop : -1.59 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 101 HIS 0.004 0.001 HIS C 203 PHE 0.033 0.002 PHE A 234 TYR 0.022 0.002 TYR D 94 ARG 0.012 0.001 ARG D 45 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 381) hydrogen bonds : angle 6.07399 ( 963) SS BOND : bond 0.00412 ( 20) SS BOND : angle 1.43782 ( 40) covalent geometry : bond 0.00638 (13345) covalent geometry : angle 0.66091 (18135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 71 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.7330 (OUTLIER) cc_final: 0.6899 (tp) REVERT: B 489 GLN cc_start: 0.8368 (mt0) cc_final: 0.8158 (mt0) REVERT: C 30 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8564 (t) REVERT: D 3 GLN cc_start: 0.8901 (mm110) cc_final: 0.8646 (mm110) REVERT: D 46 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8563 (mm-30) REVERT: E 22 CYS cc_start: -0.0669 (OUTLIER) cc_final: -0.1448 (t) REVERT: L 1 GLN cc_start: 0.7911 (tp40) cc_final: 0.7505 (tp-100) REVERT: L 107 GLN cc_start: 0.8026 (mp10) cc_final: 0.7530 (mp10) outliers start: 54 outliers final: 38 residues processed: 118 average time/residue: 0.2480 time to fit residues: 45.4199 Evaluate side-chains 104 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 63 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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 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 383 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 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 E residue 30 SER 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 85 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: 1.9990 chunk 58 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 111 optimal weight: 30.0000 chunk 76 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 159 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN A 501 HIS ** B 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.164890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.109578 restraints weight = 34533.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.110229 restraints weight = 19904.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.110058 restraints weight = 14091.937| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13365 Z= 0.155 Angle : 0.588 7.289 18175 Z= 0.310 Chirality : 0.046 0.212 1987 Planarity : 0.004 0.045 2326 Dihedral : 4.235 18.215 1774 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.40 % Favored : 94.41 % Rotamer: Outliers : 2.78 % Allowed : 21.36 % Favored : 75.85 % 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: -1.51 (0.45), residues: 123 sheet: 0.70 (0.24), residues: 502 loop : -1.57 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 101 HIS 0.003 0.001 HIS A 501 PHE 0.034 0.001 PHE A 234 TYR 0.037 0.001 TYR D 94 ARG 0.005 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.03128 ( 381) hydrogen bonds : angle 5.76940 ( 963) SS BOND : bond 0.00329 ( 20) SS BOND : angle 1.21256 ( 40) covalent geometry : bond 0.00364 (13345) covalent geometry : angle 0.58576 (18135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 70 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.7244 (OUTLIER) cc_final: 0.6810 (tp) REVERT: B 265 TYR cc_start: 0.6918 (m-80) cc_final: 0.6529 (m-80) REVERT: C 30 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8546 (t) REVERT: D 3 GLN cc_start: 0.8954 (mm110) cc_final: 0.8713 (mm110) REVERT: D 45 ARG cc_start: 0.6600 (mmm160) cc_final: 0.5861 (mmm160) REVERT: D 46 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8595 (mm-30) REVERT: E 22 CYS cc_start: -0.0709 (OUTLIER) cc_final: -0.1479 (t) REVERT: L 1 GLN cc_start: 0.7807 (tp40) cc_final: 0.7424 (tp-100) REVERT: L 107 GLN cc_start: 0.8040 (mp10) cc_final: 0.7563 (mp10) outliers start: 40 outliers final: 34 residues processed: 105 average time/residue: 0.2291 time to fit residues: 37.0983 Evaluate side-chains 100 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 63 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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 132 PHE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 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 398 ILE 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 220 GLU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 95 CYS Chi-restraints excluded: chain L residue 102 GLN 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: 2.9990 chunk 2 optimal weight: 0.5980 chunk 122 optimal weight: 20.0000 chunk 80 optimal weight: 0.0060 chunk 113 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 123 optimal weight: 40.0000 chunk 79 optimal weight: 0.7980 chunk 7 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN A 501 HIS ** B 169 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.170797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.117601 restraints weight = 35878.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.116787 restraints weight = 18885.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.116463 restraints weight = 15916.459| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13365 Z= 0.108 Angle : 0.565 7.777 18175 Z= 0.297 Chirality : 0.045 0.193 1987 Planarity : 0.004 0.045 2326 Dihedral : 3.940 17.664 1774 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.40 % Favored : 94.41 % Rotamer: Outliers : 2.23 % Allowed : 22.06 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.21), residues: 1592 helix: -1.30 (0.49), residues: 106 sheet: 0.82 (0.24), residues: 504 loop : -1.46 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 101 HIS 0.003 0.000 HIS A 501 PHE 0.032 0.001 PHE A 388 TYR 0.030 0.001 TYR D 94 ARG 0.005 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.02901 ( 381) hydrogen bonds : angle 5.55289 ( 963) SS BOND : bond 0.00295 ( 20) SS BOND : angle 1.08801 ( 40) covalent geometry : bond 0.00247 (13345) covalent geometry : angle 0.56283 (18135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 78 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.7371 (OUTLIER) cc_final: 0.6920 (tp) REVERT: B 265 TYR cc_start: 0.6918 (m-80) cc_final: 0.6544 (m-80) REVERT: B 467 GLU cc_start: 0.8808 (tp30) cc_final: 0.8299 (pp20) REVERT: B 489 GLN cc_start: 0.8216 (mt0) cc_final: 0.7964 (mt0) REVERT: C 30 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8497 (t) REVERT: C 265 TYR cc_start: 0.8256 (m-80) cc_final: 0.7382 (m-80) REVERT: D 46 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8742 (mm-30) REVERT: L 1 GLN cc_start: 0.7955 (tp40) cc_final: 0.7533 (tp-100) REVERT: L 107 GLN cc_start: 0.8065 (mp10) cc_final: 0.7777 (mp10) outliers start: 32 outliers final: 29 residues processed: 103 average time/residue: 0.2341 time to fit residues: 36.9498 Evaluate side-chains 101 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 1.491 ------------------------------------------------------------------------------- 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 132 PHE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 342 THR 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 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 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 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: 7.9990 chunk 23 optimal weight: 0.0270 chunk 72 optimal weight: 0.9990 chunk 142 optimal weight: 30.0000 chunk 39 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.1642 ------------------------------------------------------------------------------- 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 = 0.4430 r_free = 0.4430 target = 0.155972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.102811 restraints weight = 35823.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.102118 restraints weight = 19200.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.101682 restraints weight = 16135.415| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13365 Z= 0.146 Angle : 0.589 9.154 18175 Z= 0.308 Chirality : 0.045 0.192 1987 Planarity : 0.004 0.044 2326 Dihedral : 4.000 17.289 1774 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.84 % Favored : 93.97 % Rotamer: Outliers : 2.44 % Allowed : 21.99 % 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: -1.02 (0.21), residues: 1592 helix: -1.41 (0.47), residues: 111 sheet: 0.73 (0.24), residues: 518 loop : -1.46 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 101 HIS 0.002 0.000 HIS A 203 PHE 0.031 0.001 PHE A 234 TYR 0.024 0.001 TYR D 94 ARG 0.004 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.03045 ( 381) hydrogen bonds : angle 5.55725 ( 963) SS BOND : bond 0.00313 ( 20) SS BOND : angle 1.09005 ( 40) covalent geometry : bond 0.00343 (13345) covalent geometry : angle 0.58712 (18135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 73 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.6942 (tp) REVERT: A 511 PHE cc_start: 0.8202 (m-80) cc_final: 0.7894 (m-80) REVERT: B 265 TYR cc_start: 0.6919 (m-80) cc_final: 0.6559 (m-80) REVERT: B 489 GLN cc_start: 0.8284 (mt0) cc_final: 0.8024 (mt0) REVERT: C 30 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8543 (t) REVERT: C 265 TYR cc_start: 0.8233 (m-80) cc_final: 0.7357 (m-80) REVERT: D 45 ARG cc_start: 0.6519 (mmm160) cc_final: 0.6217 (mmm160) REVERT: E 22 CYS cc_start: -0.0625 (OUTLIER) cc_final: -0.1388 (t) REVERT: L 1 GLN cc_start: 0.7925 (tp40) cc_final: 0.7516 (tp-100) REVERT: L 12 VAL cc_start: 0.9238 (t) cc_final: 0.8996 (p) REVERT: L 107 GLN cc_start: 0.8037 (mp10) cc_final: 0.7715 (mp10) outliers start: 35 outliers final: 31 residues processed: 101 average time/residue: 0.2188 time to fit residues: 34.0816 Evaluate side-chains 106 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 72 time to evaluate : 1.405 ------------------------------------------------------------------------------- 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 132 PHE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 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 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 30 SER Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain L residue 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 117 optimal weight: 0.3980 chunk 39 optimal weight: 9.9990 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 65 optimal weight: 0.0570 chunk 140 optimal weight: 20.0000 chunk 21 optimal weight: 0.7980 chunk 123 optimal weight: 0.0980 chunk 135 optimal weight: 0.0050 overall best weight: 0.2712 ------------------------------------------------------------------------------- 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** ** 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 = 0.4484 r_free = 0.4484 target = 0.166868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.113255 restraints weight = 34655.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.113517 restraints weight = 19755.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.113637 restraints weight = 14438.180| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13365 Z= 0.102 Angle : 0.570 9.319 18175 Z= 0.296 Chirality : 0.045 0.179 1987 Planarity : 0.004 0.050 2326 Dihedral : 3.768 16.862 1774 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.15 % Favored : 94.66 % Rotamer: Outliers : 2.30 % Allowed : 22.20 % 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: -0.77 (0.21), residues: 1592 helix: -1.14 (0.51), residues: 100 sheet: 0.96 (0.24), residues: 505 loop : -1.32 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 101 HIS 0.002 0.000 HIS B 203 PHE 0.026 0.001 PHE A 234 TYR 0.021 0.001 TYR D 94 ARG 0.005 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.02721 ( 381) hydrogen bonds : angle 5.36623 ( 963) SS BOND : bond 0.00277 ( 20) SS BOND : angle 1.06226 ( 40) covalent geometry : bond 0.00234 (13345) covalent geometry : angle 0.56884 (18135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5535.73 seconds wall clock time: 98 minutes 7.09 seconds (5887.09 seconds total)