Starting phenix.real_space_refine on Thu Sep 18 04:52:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9atp_43832/09_2025/9atp_43832.cif Found real_map, /net/cci-nas-00/data/ceres_data/9atp_43832/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9atp_43832/09_2025/9atp_43832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9atp_43832/09_2025/9atp_43832.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9atp_43832/09_2025/9atp_43832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9atp_43832/09_2025/9atp_43832.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.19, per 1000 atoms: 0.32 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: 1.14 Conformation dependent library (CDL) restraints added in 673.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.53 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: 2.19 Time building geometry restraints manager: 1.54 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: 4.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.890 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.390 ------------------------------------------------------------------------------- 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 : 15.00 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG B 462 TYR 0.016 0.002 TYR B 166 PHE 0.038 0.002 PHE L 67 TRP 0.075 0.002 TRP B 101 HIS 0.020 0.001 HIS A 501 Details of bonding type rmsd covalent geometry : bond 0.00489 (13345) covalent geometry : angle 0.73022 (18135) SS BOND : bond 0.00727 ( 20) SS BOND : angle 1.02484 ( 40) hydrogen bonds : bond 0.11307 ( 381) hydrogen bonds : angle 7.20549 ( 963) *********************** 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 : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 98 VAL cc_start: 0.4089 (t) cc_final: 0.3529 (t) REVERT: D 103 ASP cc_start: 0.4834 (m-30) cc_final: 0.4164 (m-30) outliers start: 3 outliers final: 2 residues processed: 97 average time/residue: 0.1192 time to fit residues: 17.4168 Evaluate side-chains 82 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 50.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN B 169 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.156899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.101447 restraints weight = 35445.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.102614 restraints weight = 23091.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.102242 restraints weight = 14717.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.102945 restraints weight = 13790.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.103037 restraints weight = 12346.364| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13365 Z= 0.216 Angle : 0.635 6.901 18175 Z= 0.341 Chirality : 0.047 0.229 1987 Planarity : 0.005 0.055 2326 Dihedral : 4.676 34.916 1780 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.47 % Favored : 93.22 % Rotamer: Outliers : 2.30 % Allowed : 19.49 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.21), residues: 1592 helix: -1.94 (0.42), residues: 123 sheet: 0.46 (0.23), residues: 533 loop : -1.62 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 19 TYR 0.016 0.002 TYR A 275 PHE 0.016 0.002 PHE L 67 TRP 0.034 0.002 TRP B 101 HIS 0.007 0.001 HIS A 501 Details of bonding type rmsd covalent geometry : bond 0.00501 (13345) covalent geometry : angle 0.63442 (18135) SS BOND : bond 0.00331 ( 20) SS BOND : angle 0.98583 ( 40) hydrogen bonds : bond 0.03951 ( 381) hydrogen bonds : angle 6.30064 ( 963) *********************** 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 118 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.7020 (OUTLIER) cc_final: 0.6792 (tp) REVERT: B 101 TRP cc_start: 0.7655 (m-90) cc_final: 0.7398 (m-90) REVERT: B 467 GLU cc_start: 0.8862 (tp30) cc_final: 0.8212 (pp20) REVERT: B 515 HIS cc_start: 0.5981 (t-90) cc_final: 0.5769 (t-90) REVERT: D 46 GLU cc_start: 0.8672 (mm-30) cc_final: 0.7989 (mm-30) REVERT: L 75 LYS cc_start: 0.9233 (mmmt) cc_final: 0.8924 (mmmm) outliers start: 33 outliers final: 17 residues processed: 110 average time/residue: 0.1134 time to fit residues: 19.0888 Evaluate side-chains 90 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 44 VAL 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 237 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 111 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 29 optimal weight: 6.9990 chunk 115 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 151 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 141 optimal weight: 50.0000 chunk 60 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 HIS ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN D 5 GLN 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 = 0.4401 r_free = 0.4401 target = 0.159010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.107627 restraints weight = 36018.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.103298 restraints weight = 21741.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.103732 restraints weight = 19168.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.104056 restraints weight = 17281.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.104428 restraints weight = 14297.092| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.062 13365 Z= 0.407 Angle : 0.790 8.283 18175 Z= 0.421 Chirality : 0.052 0.219 1987 Planarity : 0.006 0.072 2326 Dihedral : 5.439 28.414 1774 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.73 % Favored : 91.96 % Rotamer: Outliers : 4.59 % Allowed : 19.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.20), residues: 1592 helix: -2.12 (0.41), residues: 122 sheet: -0.03 (0.23), residues: 516 loop : -1.86 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 210 TYR 0.028 0.002 TYR B 166 PHE 0.024 0.003 PHE A 132 TRP 0.028 0.002 TRP B 101 HIS 0.005 0.001 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00950 (13345) covalent geometry : angle 0.78775 (18135) SS BOND : bond 0.00905 ( 20) SS BOND : angle 1.40944 ( 40) hydrogen bonds : bond 0.04611 ( 381) hydrogen bonds : angle 6.69744 ( 963) *********************** 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 143 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 77 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.6865 (tp) REVERT: B 410 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8616 (mt0) REVERT: B 467 GLU cc_start: 0.8893 (tp30) cc_final: 0.8269 (pp20) REVERT: C 98 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8587 (tp) REVERT: D 46 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8569 (mm-30) REVERT: L 102 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8236 (pm20) outliers start: 66 outliers final: 32 residues processed: 137 average time/residue: 0.1122 time to fit residues: 23.3916 Evaluate side-chains 102 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 66 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 162 CYS 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 298 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 204 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 345 SER Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 455 SER 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 111 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain D residue 7 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 30.0000 chunk 31 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.162856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.109241 restraints weight = 35400.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.107492 restraints weight = 19333.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.107941 restraints weight = 17211.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.108369 restraints weight = 14460.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.108211 restraints weight = 12599.596| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3208 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= 0.214 Angle : 0.645 8.477 18175 Z= 0.342 Chirality : 0.047 0.188 1987 Planarity : 0.005 0.067 2326 Dihedral : 4.783 21.594 1774 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.84 % Favored : 93.84 % Rotamer: Outliers : 3.62 % Allowed : 20.95 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.20), residues: 1592 helix: -1.94 (0.42), residues: 122 sheet: 0.16 (0.23), residues: 521 loop : -1.85 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 45 TYR 0.021 0.002 TYR A 156 PHE 0.022 0.002 PHE A 234 TRP 0.017 0.002 TRP B 101 HIS 0.004 0.001 HIS A 501 Details of bonding type rmsd covalent geometry : bond 0.00501 (13345) covalent geometry : angle 0.64324 (18135) SS BOND : bond 0.00389 ( 20) SS BOND : angle 1.12345 ( 40) hydrogen bonds : bond 0.03663 ( 381) hydrogen bonds : angle 6.25001 ( 963) *********************** 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 124 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 72 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.7408 (OUTLIER) cc_final: 0.6893 (tp) REVERT: B 265 TYR cc_start: 0.7065 (OUTLIER) cc_final: 0.6714 (m-80) REVERT: B 467 GLU cc_start: 0.8869 (tp30) cc_final: 0.8336 (pp20) REVERT: C 108 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6816 (t70) REVERT: D 3 GLN cc_start: 0.8916 (mm110) cc_final: 0.8658 (mm-40) REVERT: L 45 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6478 (ttp-170) REVERT: L 107 GLN cc_start: 0.8004 (mp10) cc_final: 0.7671 (mp10) outliers start: 52 outliers final: 33 residues processed: 117 average time/residue: 0.1077 time to fit residues: 19.1851 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 : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 162 CYS 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 33 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 265 TYR 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 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 87 VAL Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 45 ARG 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 34 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 37 optimal weight: 0.0040 chunk 98 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 115 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 36 optimal weight: 20.0000 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.156459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.101350 restraints weight = 35385.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.103507 restraints weight = 18965.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.102741 restraints weight = 13008.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.103578 restraints weight = 12585.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.103812 restraints weight = 11137.375| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13365 Z= 0.114 Angle : 0.579 8.214 18175 Z= 0.305 Chirality : 0.045 0.185 1987 Planarity : 0.004 0.049 2326 Dihedral : 4.230 20.314 1774 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.21 % Favored : 94.54 % Rotamer: Outliers : 2.78 % Allowed : 21.57 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.20), residues: 1592 helix: -1.70 (0.44), residues: 116 sheet: 0.38 (0.23), residues: 523 loop : -1.73 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 45 TYR 0.018 0.001 TYR B 485 PHE 0.026 0.001 PHE L 67 TRP 0.019 0.001 TRP B 101 HIS 0.003 0.001 HIS A 501 Details of bonding type rmsd covalent geometry : bond 0.00257 (13345) covalent geometry : angle 0.57711 (18135) SS BOND : bond 0.00269 ( 20) SS BOND : angle 1.10583 ( 40) hydrogen bonds : bond 0.03066 ( 381) hydrogen bonds : angle 5.85849 ( 963) *********************** 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 119 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 79 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.7278 (OUTLIER) cc_final: 0.6804 (tp) REVERT: B 353 ARG cc_start: 0.8580 (ptp-110) cc_final: 0.8375 (ttm-80) REVERT: B 410 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8548 (tt0) REVERT: B 467 GLU cc_start: 0.8873 (tp30) cc_final: 0.8368 (pp20) REVERT: C 30 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8508 (t) REVERT: D 3 GLN cc_start: 0.8948 (mm110) cc_final: 0.8655 (mm-40) REVERT: D 45 ARG cc_start: 0.7554 (mmp-170) cc_final: 0.6722 (mmp-170) REVERT: D 46 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8574 (mm-30) REVERT: E 22 CYS cc_start: -0.0803 (OUTLIER) cc_final: -0.1946 (t) REVERT: E 82 MET cc_start: -0.5365 (tpp) cc_final: -0.5634 (ttt) REVERT: L 3 GLN cc_start: 0.7610 (mp10) cc_final: 0.6795 (mp10) REVERT: L 107 GLN cc_start: 0.7962 (mp10) cc_final: 0.7713 (mp10) outliers start: 40 outliers final: 24 residues processed: 112 average time/residue: 0.1154 time to fit residues: 19.0416 Evaluate side-chains 94 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 430 ILE 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 237 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain E residue 22 CYS 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 80 LEU Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 95 CYS Chi-restraints excluded: chain L residue 102 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 156 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 40 optimal weight: 0.2980 chunk 106 optimal weight: 0.5980 chunk 79 optimal weight: 0.0050 chunk 108 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN B 335 HIS B 446 ASN D 32 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.157236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.103975 restraints weight = 35855.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.102501 restraints weight = 20685.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.103534 restraints weight = 15144.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.103910 restraints weight = 12940.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.104058 restraints weight = 12004.825| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3547 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= 0.103 Angle : 0.557 7.160 18175 Z= 0.293 Chirality : 0.045 0.183 1987 Planarity : 0.004 0.046 2326 Dihedral : 3.976 20.079 1774 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.28 % Favored : 94.54 % Rotamer: Outliers : 2.51 % Allowed : 21.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.21), residues: 1592 helix: -1.62 (0.45), residues: 117 sheet: 0.59 (0.23), residues: 515 loop : -1.62 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 45 TYR 0.015 0.001 TYR B 485 PHE 0.022 0.001 PHE L 67 TRP 0.017 0.001 TRP B 101 HIS 0.002 0.000 HIS A 501 Details of bonding type rmsd covalent geometry : bond 0.00235 (13345) covalent geometry : angle 0.55533 (18135) SS BOND : bond 0.00247 ( 20) SS BOND : angle 1.08361 ( 40) hydrogen bonds : bond 0.02854 ( 381) hydrogen bonds : angle 5.67067 ( 963) *********************** 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 105 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 69 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 PHE cc_start: 0.9211 (OUTLIER) cc_final: 0.8853 (p90) REVERT: A 430 ILE cc_start: 0.7406 (OUTLIER) cc_final: 0.6937 (tp) REVERT: B 265 TYR cc_start: 0.6953 (m-80) cc_final: 0.6691 (m-80) REVERT: C 30 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8505 (t) REVERT: D 3 GLN cc_start: 0.8961 (mm110) cc_final: 0.8705 (mm-40) REVERT: D 45 ARG cc_start: 0.7753 (mmp-170) cc_final: 0.6978 (mmp-170) REVERT: D 46 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8602 (mp0) REVERT: E 22 CYS cc_start: -0.0319 (OUTLIER) cc_final: -0.1233 (t) REVERT: L 3 GLN cc_start: 0.7632 (mp10) cc_final: 0.7263 (mp10) REVERT: L 50 PHE cc_start: 0.8505 (m-10) cc_final: 0.8097 (m-80) REVERT: L 107 GLN cc_start: 0.7933 (mp10) cc_final: 0.7687 (mp10) outliers start: 36 outliers final: 21 residues processed: 102 average time/residue: 0.1063 time to fit residues: 16.6282 Evaluate side-chains 88 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 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 485 TYR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain E residue 22 CYS 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 92 optimal weight: 0.0060 chunk 96 optimal weight: 10.0000 chunk 125 optimal weight: 30.0000 chunk 157 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 138 optimal weight: 40.0000 chunk 80 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.163971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.110028 restraints weight = 34674.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.111098 restraints weight = 18218.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.110008 restraints weight = 13825.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.110709 restraints weight = 13779.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.111905 restraints weight = 11590.339| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 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 : 0.005 0.042 13365 Z= 0.196 Angle : 0.598 6.930 18175 Z= 0.317 Chirality : 0.046 0.257 1987 Planarity : 0.004 0.044 2326 Dihedral : 4.232 18.946 1774 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.09 % Favored : 93.72 % Rotamer: Outliers : 3.20 % Allowed : 20.88 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.21), residues: 1592 helix: -1.63 (0.44), residues: 123 sheet: 0.43 (0.23), residues: 509 loop : -1.65 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 45 TYR 0.017 0.001 TYR B 485 PHE 0.023 0.002 PHE L 67 TRP 0.018 0.001 TRP B 101 HIS 0.003 0.001 HIS A 501 Details of bonding type rmsd covalent geometry : bond 0.00458 (13345) covalent geometry : angle 0.59544 (18135) SS BOND : bond 0.00803 ( 20) SS BOND : angle 1.27137 ( 40) hydrogen bonds : bond 0.03307 ( 381) hydrogen bonds : angle 5.88181 ( 963) *********************** 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 114 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 68 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8931 (mp) REVERT: A 430 ILE cc_start: 0.7317 (OUTLIER) cc_final: 0.6853 (tp) REVERT: B 265 TYR cc_start: 0.6939 (m-80) cc_final: 0.6635 (m-80) REVERT: B 410 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8558 (mt0) REVERT: C 30 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8618 (t) REVERT: C 108 ASP cc_start: 0.7249 (OUTLIER) cc_final: 0.7031 (t70) REVERT: D 3 GLN cc_start: 0.8968 (mm110) cc_final: 0.8730 (mm110) REVERT: D 45 ARG cc_start: 0.7674 (mmp-170) cc_final: 0.7026 (mmp-170) REVERT: E 22 CYS cc_start: -0.0386 (OUTLIER) cc_final: -0.1141 (t) REVERT: E 45 ARG cc_start: -0.0765 (OUTLIER) cc_final: -0.1212 (mpt180) REVERT: L 107 GLN cc_start: 0.7914 (mp10) cc_final: 0.7397 (mp10) outliers start: 46 outliers final: 26 residues processed: 107 average time/residue: 0.1184 time to fit residues: 18.8369 Evaluate side-chains 95 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 62 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 238 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 48 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 95 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 129 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 125 optimal weight: 50.0000 chunk 91 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 114 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 1 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 = 0.4466 r_free = 0.4466 target = 0.167518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.111840 restraints weight = 33811.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.112233 restraints weight = 18160.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.112322 restraints weight = 13374.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.112777 restraints weight = 13005.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.112956 restraints weight = 11226.811| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13365 Z= 0.117 Angle : 0.562 7.507 18175 Z= 0.296 Chirality : 0.045 0.209 1987 Planarity : 0.004 0.044 2326 Dihedral : 3.995 18.657 1774 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.15 % Favored : 94.66 % Rotamer: Outliers : 2.78 % Allowed : 21.29 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.21), residues: 1592 helix: -1.46 (0.47), residues: 111 sheet: 0.62 (0.24), residues: 495 loop : -1.54 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 45 TYR 0.016 0.001 TYR B 485 PHE 0.029 0.001 PHE A 234 TRP 0.017 0.001 TRP B 101 HIS 0.002 0.000 HIS A 501 Details of bonding type rmsd covalent geometry : bond 0.00271 (13345) covalent geometry : angle 0.56026 (18135) SS BOND : bond 0.00318 ( 20) SS BOND : angle 1.09076 ( 40) hydrogen bonds : bond 0.02873 ( 381) hydrogen bonds : angle 5.63616 ( 963) *********************** 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 107 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 67 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8868 (mp) REVERT: A 430 ILE cc_start: 0.7188 (OUTLIER) cc_final: 0.6782 (tp) REVERT: B 265 TYR cc_start: 0.6957 (m-80) cc_final: 0.6677 (m-80) REVERT: B 410 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8522 (tt0) REVERT: C 30 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8504 (t) REVERT: D 3 GLN cc_start: 0.8949 (mm110) cc_final: 0.8744 (mm110) REVERT: D 45 ARG cc_start: 0.7638 (mmp-170) cc_final: 0.6391 (mmp-170) REVERT: D 46 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8644 (mp0) REVERT: E 22 CYS cc_start: -0.0871 (OUTLIER) cc_final: -0.1632 (t) REVERT: E 45 ARG cc_start: -0.0752 (OUTLIER) cc_final: -0.1197 (mpt180) REVERT: L 1 GLN cc_start: 0.8366 (tp40) cc_final: 0.8038 (tp-100) REVERT: L 3 GLN cc_start: 0.8082 (mp10) cc_final: 0.7361 (mp10) REVERT: L 107 GLN cc_start: 0.7877 (mp10) cc_final: 0.7649 (mp10) outliers start: 40 outliers final: 27 residues processed: 103 average time/residue: 0.1159 time to fit residues: 18.0152 Evaluate side-chains 97 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 64 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 238 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 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 410 GLN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 95 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 24 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 138 optimal weight: 40.0000 chunk 64 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 136 optimal weight: 30.0000 chunk 102 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 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 = 0.4414 r_free = 0.4414 target = 0.159590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.108618 restraints weight = 35333.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.103521 restraints weight = 19399.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.104703 restraints weight = 18138.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.105195 restraints weight = 13877.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.105267 restraints weight = 12219.323| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 13365 Z= 0.284 Angle : 0.668 8.615 18175 Z= 0.354 Chirality : 0.048 0.213 1987 Planarity : 0.005 0.045 2326 Dihedral : 4.561 18.612 1774 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.66 % Favored : 93.09 % Rotamer: Outliers : 3.06 % Allowed : 21.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.20), residues: 1592 helix: -1.61 (0.45), residues: 122 sheet: 0.23 (0.24), residues: 481 loop : -1.67 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 45 TYR 0.022 0.002 TYR A 166 PHE 0.030 0.002 PHE A 234 TRP 0.018 0.001 TRP B 101 HIS 0.004 0.001 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00662 (13345) covalent geometry : angle 0.66628 (18135) SS BOND : bond 0.00443 ( 20) SS BOND : angle 1.29885 ( 40) hydrogen bonds : bond 0.03773 ( 381) hydrogen bonds : angle 6.06005 ( 963) *********************** 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 112 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 68 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8906 (mp) REVERT: A 430 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7231 (tp) REVERT: B 265 TYR cc_start: 0.7007 (m-80) cc_final: 0.6624 (m-80) REVERT: B 410 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8676 (mt0) REVERT: C 30 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8584 (t) REVERT: D 3 GLN cc_start: 0.9000 (mm110) cc_final: 0.8715 (mm110) REVERT: D 45 ARG cc_start: 0.7664 (mmp-170) cc_final: 0.6832 (mmp-170) REVERT: E 22 CYS cc_start: -0.0290 (OUTLIER) cc_final: -0.1066 (t) REVERT: E 45 ARG cc_start: -0.0694 (OUTLIER) cc_final: -0.1220 (mpt180) REVERT: L 1 GLN cc_start: 0.8238 (tp40) cc_final: 0.7977 (tp-100) REVERT: L 3 GLN cc_start: 0.8118 (mp10) cc_final: 0.7345 (mp10) REVERT: L 75 LYS cc_start: 0.9214 (mmmm) cc_final: 0.8996 (mmmm) outliers start: 44 outliers final: 32 residues processed: 110 average time/residue: 0.1120 time to fit residues: 18.5225 Evaluate side-chains 100 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 62 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 238 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 39 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 95 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 142 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 152 optimal weight: 0.3980 chunk 120 optimal weight: 20.0000 chunk 117 optimal weight: 0.0270 chunk 116 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 149 optimal weight: 6.9990 overall best weight: 1.2442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN D 107 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.163754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.110200 restraints weight = 34790.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.110409 restraints weight = 17790.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.110280 restraints weight = 13079.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.110761 restraints weight = 12907.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.111125 restraints weight = 11062.583| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13365 Z= 0.153 Angle : 0.606 9.239 18175 Z= 0.317 Chirality : 0.046 0.201 1987 Planarity : 0.004 0.045 2326 Dihedral : 4.249 17.936 1774 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.40 % Favored : 94.41 % Rotamer: Outliers : 2.71 % Allowed : 22.27 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.21), residues: 1592 helix: -1.52 (0.45), residues: 123 sheet: 0.42 (0.24), residues: 503 loop : -1.68 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 45 TYR 0.017 0.001 TYR B 485 PHE 0.030 0.001 PHE A 234 TRP 0.021 0.001 TRP B 101 HIS 0.002 0.001 HIS A 501 Details of bonding type rmsd covalent geometry : bond 0.00359 (13345) covalent geometry : angle 0.60393 (18135) SS BOND : bond 0.00332 ( 20) SS BOND : angle 1.12623 ( 40) hydrogen bonds : bond 0.03075 ( 381) hydrogen bonds : angle 5.76541 ( 963) ********************** 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 107 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 68 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8890 (mp) REVERT: A 430 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7111 (tp) REVERT: B 265 TYR cc_start: 0.7015 (m-80) cc_final: 0.6697 (m-80) REVERT: B 410 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8549 (mt0) REVERT: B 489 GLN cc_start: 0.8269 (mt0) cc_final: 0.8056 (mt0) REVERT: C 30 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8554 (t) REVERT: D 3 GLN cc_start: 0.9078 (mm110) cc_final: 0.8830 (mm110) REVERT: D 45 ARG cc_start: 0.7509 (mmp-170) cc_final: 0.6107 (mmp-170) REVERT: D 46 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8717 (mp0) REVERT: E 22 CYS cc_start: -0.0450 (OUTLIER) cc_final: -0.1209 (t) REVERT: E 45 ARG cc_start: -0.0760 (OUTLIER) cc_final: -0.1249 (mpt180) REVERT: L 1 GLN cc_start: 0.8240 (tp40) cc_final: 0.7861 (tp-100) REVERT: L 107 GLN cc_start: 0.7908 (mp10) cc_final: 0.7646 (mp10) outliers start: 39 outliers final: 32 residues processed: 104 average time/residue: 0.1144 time to fit residues: 17.9122 Evaluate side-chains 104 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 66 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 238 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 39 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 95 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 59 optimal weight: 0.2980 chunk 76 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 15 optimal weight: 0.3980 chunk 119 optimal weight: 0.8980 chunk 112 optimal weight: 30.0000 chunk 125 optimal weight: 30.0000 chunk 83 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 99 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.165318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.109440 restraints weight = 34360.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.112134 restraints weight = 19456.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.111221 restraints weight = 12340.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.111741 restraints weight = 12818.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.111902 restraints weight = 10783.676| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13365 Z= 0.110 Angle : 0.577 8.931 18175 Z= 0.301 Chirality : 0.045 0.188 1987 Planarity : 0.004 0.044 2326 Dihedral : 3.911 17.715 1774 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.84 % Favored : 94.97 % Rotamer: Outliers : 2.57 % Allowed : 22.48 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.21), residues: 1592 helix: -1.31 (0.49), residues: 105 sheet: 0.66 (0.24), residues: 487 loop : -1.55 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 45 TYR 0.016 0.001 TYR B 485 PHE 0.025 0.001 PHE A 234 TRP 0.018 0.001 TRP B 101 HIS 0.002 0.000 HIS A 501 Details of bonding type rmsd covalent geometry : bond 0.00254 (13345) covalent geometry : angle 0.57585 (18135) SS BOND : bond 0.00289 ( 20) SS BOND : angle 1.02006 ( 40) hydrogen bonds : bond 0.02786 ( 381) hydrogen bonds : angle 5.52749 ( 963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2722.61 seconds wall clock time: 47 minutes 43.92 seconds (2863.92 seconds total)