Starting phenix.real_space_refine on Thu Jul 2 22:33:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7a5r_11648/07_2026/7a5r_11648.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a5r_11648/07_2026/7a5r_11648.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7a5r_11648/07_2026/7a5r_11648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a5r_11648/07_2026/7a5r_11648.map" model { file = "/net/cci-nas-00/data/ceres_data/7a5r_11648/07_2026/7a5r_11648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a5r_11648/07_2026/7a5r_11648.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7a5r_11648/07_2026/7a5r_11648.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7a5r_11648/07_2026/7a5r_11648.cif" } resolution = 3.7 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= 0.002 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 6760 2.51 5 N 1748 2.21 5 O 2060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10608 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1595 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 198} Chain breaks: 1 Chain: "L" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1568 Classifications: {'peptide': 202} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 190} Chain breaks: 2 Chain: "A" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2113 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 17, 'TRANS': 246} Chain breaks: 4 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: I, M, B, D Time building chain proxies: 2.86, per 1000 atoms: 0.27 Number of scatterers: 10608 At special positions: 0 Unit cell: (138.049, 166.311, 71.742, 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 40 16.00 O 2060 8.00 N 1748 7.00 C 6760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Simple disulfide: pdb=" SG CYS L 140 " - pdb=" SG CYS L 200 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 200 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 94 " distance=2.04 Simple disulfide: pdb=" SG CYS M 140 " - pdb=" SG CYS M 200 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 343 " " NAG D 1 " - " ASN B 343 " Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 233.9 milliseconds 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 30 sheets defined 6.8% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'L' and resid 127 through 134 removed outlier: 3.689A pdb=" N LEU L 131 " --> pdb=" O SER L 127 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS L 132 " --> pdb=" O ASP L 128 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER L 133 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY L 134 " --> pdb=" O GLN L 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 127 through 134' Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.964A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 369' Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.237A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.759A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.783A pdb=" N ASP A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 369 removed outlier: 3.964A pdb=" N LEU B 368 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 369' Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.238A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.758A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.783A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 134 removed outlier: 3.690A pdb=" N LEU M 131 " --> pdb=" O SER M 127 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS M 132 " --> pdb=" O ASP M 128 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER M 133 " --> pdb=" O GLU M 129 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY M 134 " --> pdb=" O GLN M 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 127 through 134' Processing helix chain 'I' and resid 160 through 162 No H-bonds generated for 'chain 'I' and resid 160 through 162' Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.749A pdb=" N GLU H 10 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR H 116 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.749A pdb=" N GLU H 10 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR H 116 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL H 108 " --> pdb=" O GLY H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 124 through 128 removed outlier: 4.342A pdb=" N GLY H 143 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS H 144 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER H 184 " --> pdb=" O CYS H 144 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP H 148 " --> pdb=" O TYR H 180 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 155 through 158 removed outlier: 4.747A pdb=" N TYR H 198 " --> pdb=" O VAL H 215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.247A pdb=" N LEU L 11 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.772A pdb=" N LYS L 36 " --> pdb=" O TYR L 31 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 120 through 124 removed outlier: 3.879A pdb=" N SER L 120 " --> pdb=" O ASN L 143 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN L 143 " --> pdb=" O SER L 120 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 150 through 156 removed outlier: 3.637A pdb=" N TYR L 198 " --> pdb=" O PHE L 215 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.512A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 277 " --> pdb=" O HIS A 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AB4, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.912A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB6, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB7, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.512A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 277 " --> pdb=" O HIS B 49 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AB9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.912A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC3, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.247A pdb=" N LEU M 11 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP M 41 " --> pdb=" O LEU M 53 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 30 through 31 removed outlier: 3.773A pdb=" N LYS M 36 " --> pdb=" O TYR M 31 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 120 through 124 removed outlier: 3.879A pdb=" N SER M 120 " --> pdb=" O ASN M 143 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN M 143 " --> pdb=" O SER M 120 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 150 through 156 removed outlier: 3.637A pdb=" N TYR M 198 " --> pdb=" O PHE M 215 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.749A pdb=" N GLU I 10 " --> pdb=" O THR I 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR I 116 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.749A pdb=" N GLU I 10 " --> pdb=" O THR I 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR I 116 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL I 108 " --> pdb=" O GLY I 98 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 124 through 128 removed outlier: 4.343A pdb=" N GLY I 143 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS I 144 " --> pdb=" O SER I 184 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER I 184 " --> pdb=" O CYS I 144 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP I 148 " --> pdb=" O TYR I 180 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR I 180 " --> pdb=" O ASP I 148 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 155 through 158 removed outlier: 4.747A pdb=" N TYR I 198 " --> pdb=" O VAL I 215 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 792 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: 1.64 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3324 1.34 - 1.46: 2768 1.46 - 1.58: 4730 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 10870 Sorted by residual: bond pdb=" N LEU H 174 " pdb=" CA LEU H 174 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.24e-02 6.50e+03 5.14e+00 bond pdb=" N LEU I 174 " pdb=" CA LEU I 174 " ideal model delta sigma weight residual 1.458 1.484 -0.027 1.24e-02 6.50e+03 4.60e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.44e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.13e+00 ... (remaining 10865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 14062 1.68 - 3.36: 608 3.36 - 5.05: 92 5.05 - 6.73: 14 6.73 - 8.41: 10 Bond angle restraints: 14786 Sorted by residual: angle pdb=" C ASN B 370 " pdb=" CA ASN B 370 " pdb=" CB ASN B 370 " ideal model delta sigma weight residual 111.91 116.08 -4.17 1.52e+00 4.33e-01 7.53e+00 angle pdb=" CA ILE M 2 " pdb=" CB ILE M 2 " pdb=" CG1 ILE M 2 " ideal model delta sigma weight residual 110.40 115.06 -4.66 1.70e+00 3.46e-01 7.51e+00 angle pdb=" CA ILE L 2 " pdb=" CB ILE L 2 " pdb=" CG1 ILE L 2 " ideal model delta sigma weight residual 110.40 115.04 -4.64 1.70e+00 3.46e-01 7.45e+00 angle pdb=" C ASN A 370 " pdb=" CA ASN A 370 " pdb=" CB ASN A 370 " ideal model delta sigma weight residual 111.91 116.05 -4.14 1.52e+00 4.33e-01 7.42e+00 angle pdb=" C TYR M 146 " pdb=" N PRO M 147 " pdb=" CA PRO M 147 " ideal model delta sigma weight residual 127.00 133.25 -6.25 2.40e+00 1.74e-01 6.78e+00 ... (remaining 14781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 5815 17.87 - 35.75: 497 35.75 - 53.62: 98 53.62 - 71.49: 22 71.49 - 89.37: 6 Dihedral angle restraints: 6438 sinusoidal: 2500 harmonic: 3938 Sorted by residual: dihedral pdb=" CB CYS H 144 " pdb=" SG CYS H 144 " pdb=" SG CYS H 200 " pdb=" CB CYS H 200 " ideal model delta sinusoidal sigma weight residual 93.00 129.54 -36.54 1 1.00e+01 1.00e-02 1.89e+01 dihedral pdb=" CB CYS I 144 " pdb=" SG CYS I 144 " pdb=" SG CYS I 200 " pdb=" CB CYS I 200 " ideal model delta sinusoidal sigma weight residual 93.00 129.53 -36.53 1 1.00e+01 1.00e-02 1.89e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual -86.00 -122.12 36.12 1 1.00e+01 1.00e-02 1.85e+01 ... (remaining 6435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 964 0.035 - 0.069: 406 0.069 - 0.104: 190 0.104 - 0.138: 83 0.138 - 0.173: 9 Chirality restraints: 1652 Sorted by residual: chirality pdb=" CB ILE L 34 " pdb=" CA ILE L 34 " pdb=" CG1 ILE L 34 " pdb=" CG2 ILE L 34 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.44e-01 chirality pdb=" CB ILE M 34 " pdb=" CA ILE M 34 " pdb=" CG1 ILE M 34 " pdb=" CG2 ILE M 34 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CB THR I 91 " pdb=" CA THR I 91 " pdb=" OG1 THR I 91 " pdb=" CG2 THR I 91 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.31e-01 ... (remaining 1649 not shown) Planarity restraints: 1884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 152 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO H 153 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO H 153 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 153 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU I 152 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO I 153 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO I 153 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO I 153 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 512 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C VAL B 512 " 0.030 2.00e-02 2.50e+03 pdb=" O VAL B 512 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU B 513 " -0.010 2.00e-02 2.50e+03 ... (remaining 1881 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1233 2.75 - 3.29: 9288 3.29 - 3.83: 15432 3.83 - 4.36: 17584 4.36 - 4.90: 32591 Nonbonded interactions: 76128 Sorted by model distance: nonbonded pdb=" OG SER M 127 " pdb=" NZ LYS I 218 " model vdw 2.218 3.120 nonbonded pdb=" OG SER M 120 " pdb=" OD1 ASN M 143 " model vdw 2.381 3.040 nonbonded pdb=" OG SER L 120 " pdb=" OD1 ASN L 143 " model vdw 2.381 3.040 nonbonded pdb=" NZ LYS H 218 " pdb=" OG SER L 127 " model vdw 2.405 3.120 nonbonded pdb=" O LEU H 174 " pdb=" CD1 LEU H 174 " model vdw 2.418 3.460 ... (remaining 76123 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: 0.03 Found NCS groups: ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 4.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.640 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 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 : 0.004 0.038 10890 Z= 0.187 Angle : 0.812 8.411 14830 Z= 0.437 Chirality : 0.050 0.173 1652 Planarity : 0.005 0.051 1882 Dihedral : 13.987 89.368 3870 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.59 % Favored : 92.26 % Rotamer: Outliers : 0.67 % Allowed : 6.13 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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 are not related in a simple way. whole: -1.97 (0.22), residues: 1318 helix: -2.70 (0.69), residues: 52 sheet: 0.16 (0.24), residues: 482 loop : -2.31 (0.19), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 328 TYR 0.019 0.002 TYR B 351 PHE 0.017 0.002 PHE H 29 TRP 0.027 0.002 TRP H 83 HIS 0.002 0.001 HIS L 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (10870) covalent geometry : angle 0.80927 / 0.44 (14786) SS BOND : bond 0.00529 / 0.31 ( 16) SS BOND : angle 1.17870 / 0.77 ( 32) hydrogen bonds : bond 0.14114 / 9.59 ( 314) hydrogen bonds : angle 8.09289 / 5.48 ( 792) link_BETA1-4 : bond 0.00256 / 0.13 ( 2) link_BETA1-4 : angle 1.30712 / 0.90 ( 6) link_NAG-ASN : bond 0.00025 / 0.01 ( 2) link_NAG-ASN : angle 2.39084 / 1.85 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 0.440 Fit side-chains REVERT: H 142 LEU cc_start: 0.7623 (pp) cc_final: 0.7406 (pp) REVERT: L 132 LYS cc_start: 0.8278 (mttt) cc_final: 0.8055 (pttm) REVERT: M 51 LYS cc_start: 0.8025 (mttt) cc_final: 0.7779 (tttm) REVERT: M 132 LYS cc_start: 0.7935 (mttt) cc_final: 0.7720 (pttm) REVERT: I 6 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8179 (mt0) REVERT: I 38 ARG cc_start: 0.8999 (ptm-80) cc_final: 0.8687 (ptm-80) REVERT: I 142 LEU cc_start: 0.7429 (pp) cc_final: 0.7228 (pp) outliers start: 8 outliers final: 4 residues processed: 179 average time/residue: 0.1192 time to fit residues: 28.8482 Evaluate side-chains 121 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain I residue 6 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0170 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN H 77 ASN L 35 ASN L 44 GLN L 106 GLN A 49 HIS A 271 GLN B 271 GLN B 493 GLN M 35 ASN M 44 GLN M 106 GLN I 77 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.135548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.118981 restraints weight = 16636.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.120392 restraints weight = 13139.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.121393 restraints weight = 11099.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.121759 restraints weight = 9771.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.122423 restraints weight = 9127.054| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10890 Z= 0.167 Angle : 0.695 8.256 14830 Z= 0.359 Chirality : 0.047 0.144 1652 Planarity : 0.005 0.040 1882 Dihedral : 5.498 59.702 1469 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.18 % Allowed : 8.99 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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 are not related in a simple way. whole: -1.48 (0.22), residues: 1318 helix: -3.08 (0.75), residues: 40 sheet: 0.59 (0.23), residues: 508 loop : -2.10 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 408 TYR 0.015 0.002 TYR I 180 PHE 0.017 0.002 PHE L 122 TRP 0.016 0.002 TRP I 83 HIS 0.004 0.001 HIS I 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (10870) covalent geometry : angle 0.69273 / 0.36 (14786) SS BOND : bond 0.00534 / 0.30 ( 16) SS BOND : angle 1.08571 / 0.70 ( 32) hydrogen bonds : bond 0.04218 / 2.87 ( 314) hydrogen bonds : angle 6.66301 / 4.51 ( 792) link_BETA1-4 : bond 0.00310 / 0.16 ( 2) link_BETA1-4 : angle 0.95403 / 0.68 ( 6) link_NAG-ASN : bond 0.00006 / 0.00 ( 2) link_NAG-ASN : angle 1.66075 / 1.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: H 142 LEU cc_start: 0.7524 (pp) cc_final: 0.7253 (pp) REVERT: A 471 GLU cc_start: 0.4875 (OUTLIER) cc_final: 0.4342 (tp30) REVERT: A 489 TYR cc_start: 0.8784 (m-80) cc_final: 0.8505 (m-80) REVERT: B 471 GLU cc_start: 0.4692 (OUTLIER) cc_final: 0.4254 (tp30) REVERT: I 142 LEU cc_start: 0.7446 (pp) cc_final: 0.7234 (pp) outliers start: 26 outliers final: 15 residues processed: 132 average time/residue: 0.0992 time to fit residues: 18.1858 Evaluate side-chains 122 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 184 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 34 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN A 493 GLN B 493 GLN I 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.132476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.116145 restraints weight = 16868.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.117363 restraints weight = 13612.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.118298 restraints weight = 11649.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.118959 restraints weight = 10398.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.119288 restraints weight = 9556.077| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10890 Z= 0.170 Angle : 0.657 8.780 14830 Z= 0.337 Chirality : 0.046 0.149 1652 Planarity : 0.005 0.042 1882 Dihedral : 5.174 57.171 1466 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.69 % Allowed : 13.28 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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 are not related in a simple way. whole: -1.35 (0.22), residues: 1318 helix: -4.19 (0.55), residues: 40 sheet: 0.66 (0.23), residues: 514 loop : -1.94 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 403 TYR 0.019 0.002 TYR I 180 PHE 0.018 0.002 PHE L 122 TRP 0.012 0.002 TRP B 353 HIS 0.004 0.001 HIS H 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 (10870) covalent geometry : angle 0.65498 / 0.34 (14786) SS BOND : bond 0.00571 / 0.32 ( 16) SS BOND : angle 1.12503 / 0.71 ( 32) hydrogen bonds : bond 0.03982 / 2.72 ( 314) hydrogen bonds : angle 6.12014 / 4.15 ( 792) link_BETA1-4 : bond 0.00331 / 0.17 ( 2) link_BETA1-4 : angle 0.98849 / 0.69 ( 6) link_NAG-ASN : bond 0.00090 / 0.05 ( 2) link_NAG-ASN : angle 1.28507 / 1.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: H 2 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6162 (ppp) REVERT: H 142 LEU cc_start: 0.7524 (pp) cc_final: 0.7249 (pp) REVERT: L 149 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7973 (tm-30) REVERT: A 471 GLU cc_start: 0.5000 (OUTLIER) cc_final: 0.4420 (tp30) REVERT: B 471 GLU cc_start: 0.4958 (OUTLIER) cc_final: 0.4484 (tp30) REVERT: M 149 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7852 (tm-30) REVERT: M 155 LYS cc_start: 0.7386 (mmmt) cc_final: 0.6979 (mmmt) REVERT: I 2 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.6276 (ppp) REVERT: I 67 GLN cc_start: 0.8485 (mm-40) cc_final: 0.7535 (mt0) REVERT: I 142 LEU cc_start: 0.7616 (pp) cc_final: 0.7353 (pp) REVERT: I 201 ASN cc_start: 0.7631 (OUTLIER) cc_final: 0.7387 (m-40) outliers start: 32 outliers final: 19 residues processed: 132 average time/residue: 0.0900 time to fit residues: 16.9313 Evaluate side-chains 123 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 201 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 40 optimal weight: 0.4980 chunk 95 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 133 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN A 422 ASN A 493 GLN B 422 ASN B 493 GLN M 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.133049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.118670 restraints weight = 16940.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.118863 restraints weight = 15471.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.119085 restraints weight = 14237.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.119432 restraints weight = 13580.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.119509 restraints weight = 12859.910| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10890 Z= 0.151 Angle : 0.618 8.190 14830 Z= 0.315 Chirality : 0.045 0.158 1652 Planarity : 0.004 0.042 1882 Dihedral : 4.903 48.411 1463 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.61 % Allowed : 13.36 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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 are not related in a simple way. whole: -1.29 (0.22), residues: 1318 helix: -4.27 (0.56), residues: 40 sheet: 0.71 (0.23), residues: 514 loop : -1.90 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 114 TYR 0.015 0.001 TYR I 180 PHE 0.015 0.002 PHE L 122 TRP 0.012 0.001 TRP A 436 HIS 0.003 0.001 HIS H 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (10870) covalent geometry : angle 0.61555 / 0.31 (14786) SS BOND : bond 0.00534 / 0.29 ( 16) SS BOND : angle 1.15220 / 0.72 ( 32) hydrogen bonds : bond 0.03563 / 2.45 ( 314) hydrogen bonds : angle 5.87044 / 3.99 ( 792) link_BETA1-4 : bond 0.00339 / 0.17 ( 2) link_BETA1-4 : angle 1.00180 / 0.71 ( 6) link_NAG-ASN : bond 0.00111 / 0.06 ( 2) link_NAG-ASN : angle 1.19515 / 0.98 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 103 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: H 142 LEU cc_start: 0.7464 (pp) cc_final: 0.7241 (pp) REVERT: L 31 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.7244 (t80) REVERT: L 149 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7703 (tm-30) REVERT: A 471 GLU cc_start: 0.5072 (OUTLIER) cc_final: 0.4575 (tp30) REVERT: B 471 GLU cc_start: 0.5009 (OUTLIER) cc_final: 0.4614 (tp30) REVERT: M 31 TYR cc_start: 0.8319 (OUTLIER) cc_final: 0.6538 (t80) REVERT: M 149 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7750 (tm-30) REVERT: M 155 LYS cc_start: 0.7200 (mmmt) cc_final: 0.6915 (mmmt) REVERT: I 67 GLN cc_start: 0.8488 (mm-40) cc_final: 0.7669 (mt0) REVERT: I 142 LEU cc_start: 0.7562 (pp) cc_final: 0.7323 (pp) outliers start: 43 outliers final: 28 residues processed: 138 average time/residue: 0.0865 time to fit residues: 17.0527 Evaluate side-chains 128 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 181 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 184 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 130 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN A 370 ASN A 493 GLN B 370 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.128552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.113916 restraints weight = 17029.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.113966 restraints weight = 15995.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.114147 restraints weight = 15008.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.114377 restraints weight = 14509.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.114472 restraints weight = 13941.342| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 10890 Z= 0.287 Angle : 0.749 9.019 14830 Z= 0.386 Chirality : 0.049 0.163 1652 Planarity : 0.005 0.045 1882 Dihedral : 5.374 46.404 1463 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.20 % Allowed : 14.54 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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 are not related in a simple way. whole: -1.60 (0.22), residues: 1318 helix: -4.29 (0.64), residues: 40 sheet: 0.51 (0.23), residues: 520 loop : -2.16 (0.20), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 457 TYR 0.025 0.002 TYR H 180 PHE 0.035 0.003 PHE H 126 TRP 0.014 0.002 TRP A 353 HIS 0.005 0.002 HIS I 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00715 / 0.29 (10870) covalent geometry : angle 0.74241 / 0.38 (14786) SS BOND : bond 0.00778 / 0.44 ( 16) SS BOND : angle 2.19691 / 1.35 ( 32) hydrogen bonds : bond 0.04659 / 3.19 ( 314) hydrogen bonds : angle 6.18265 / 4.24 ( 792) link_BETA1-4 : bond 0.00023 / 0.01 ( 2) link_BETA1-4 : angle 1.24706 / 0.82 ( 6) link_NAG-ASN : bond 0.00118 / 0.06 ( 2) link_NAG-ASN : angle 1.59261 / 1.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 97 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: H 2 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.6368 (ppp) REVERT: H 67 GLN cc_start: 0.8670 (mm110) cc_final: 0.8423 (mm110) REVERT: H 142 LEU cc_start: 0.7596 (pp) cc_final: 0.7357 (pp) REVERT: L 31 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.7124 (t80) REVERT: L 114 ARG cc_start: 0.7315 (ptm-80) cc_final: 0.7061 (ptm160) REVERT: L 149 GLU cc_start: 0.8262 (tm-30) cc_final: 0.8021 (tm-30) REVERT: A 471 GLU cc_start: 0.5216 (OUTLIER) cc_final: 0.4637 (tp30) REVERT: B 471 GLU cc_start: 0.5126 (OUTLIER) cc_final: 0.4604 (tp30) REVERT: M 31 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.6312 (t80) REVERT: M 51 LYS cc_start: 0.8241 (mttt) cc_final: 0.7836 (tttm) REVERT: M 149 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8012 (tm-30) REVERT: M 155 LYS cc_start: 0.7318 (mmmt) cc_final: 0.6956 (mmmt) REVERT: I 2 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.6448 (ppp) REVERT: I 16 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7503 (mt-10) REVERT: I 67 GLN cc_start: 0.8520 (mm-40) cc_final: 0.7682 (mt0) REVERT: I 142 LEU cc_start: 0.7712 (pp) cc_final: 0.7467 (pp) outliers start: 50 outliers final: 37 residues processed: 140 average time/residue: 0.0898 time to fit residues: 18.4976 Evaluate side-chains 135 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 92 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 181 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 185 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 85 optimal weight: 0.3980 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 119 optimal weight: 0.0770 chunk 32 optimal weight: 0.1980 chunk 26 optimal weight: 0.6980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 196 GLN L 6 GLN A 493 GLN B 493 GLN B 542 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.131931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.117276 restraints weight = 16705.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.117524 restraints weight = 15785.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.117637 restraints weight = 14260.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.118019 restraints weight = 13687.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.118058 restraints weight = 12958.409| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10890 Z= 0.117 Angle : 0.600 8.846 14830 Z= 0.305 Chirality : 0.044 0.201 1652 Planarity : 0.004 0.044 1882 Dihedral : 4.994 49.043 1463 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.61 % Allowed : 16.22 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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 are not related in a simple way. whole: -1.38 (0.22), residues: 1318 helix: -4.09 (0.55), residues: 52 sheet: 0.64 (0.23), residues: 522 loop : -1.95 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 454 TYR 0.013 0.001 TYR L 55 PHE 0.012 0.001 PHE H 126 TRP 0.012 0.001 TRP B 436 HIS 0.001 0.001 HIS I 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (10870) covalent geometry : angle 0.59579 / 0.30 (14786) SS BOND : bond 0.00635 / 0.32 ( 16) SS BOND : angle 1.51079 / 0.94 ( 32) hydrogen bonds : bond 0.03248 / 2.24 ( 314) hydrogen bonds : angle 5.75996 / 3.93 ( 792) link_BETA1-4 : bond 0.00344 / 0.18 ( 2) link_BETA1-4 : angle 0.88730 / 0.69 ( 6) link_NAG-ASN : bond 0.00193 / 0.10 ( 2) link_NAG-ASN : angle 1.30243 / 1.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 104 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: H 2 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.6392 (ppp) REVERT: H 67 GLN cc_start: 0.8628 (mm110) cc_final: 0.8365 (mm110) REVERT: H 142 LEU cc_start: 0.7548 (pp) cc_final: 0.7333 (pp) REVERT: L 31 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.7045 (t80) REVERT: L 114 ARG cc_start: 0.7214 (ptm-80) cc_final: 0.6900 (ptm160) REVERT: L 149 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7739 (tm-30) REVERT: L 155 LYS cc_start: 0.7246 (mmmt) cc_final: 0.6898 (mmmt) REVERT: A 471 GLU cc_start: 0.5148 (OUTLIER) cc_final: 0.4727 (tp30) REVERT: B 471 GLU cc_start: 0.5151 (OUTLIER) cc_final: 0.4720 (tp30) REVERT: M 31 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.6422 (t80) REVERT: M 149 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7805 (tm-30) REVERT: M 155 LYS cc_start: 0.7167 (mmmt) cc_final: 0.6874 (mmmt) REVERT: I 67 GLN cc_start: 0.8527 (mm-40) cc_final: 0.7714 (mt0) outliers start: 43 outliers final: 32 residues processed: 140 average time/residue: 0.1023 time to fit residues: 20.3795 Evaluate side-chains 134 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 181 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 201 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 86 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 0.0030 chunk 100 optimal weight: 2.9990 chunk 81 optimal weight: 0.0670 chunk 95 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.0040 chunk 131 optimal weight: 0.0270 chunk 47 optimal weight: 0.0370 chunk 27 optimal weight: 1.9990 overall best weight: 0.0276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN A 542 ASN M 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.138923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.124116 restraints weight = 16318.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.124486 restraints weight = 14438.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.124755 restraints weight = 12911.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.125024 restraints weight = 12298.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.125064 restraints weight = 11721.281| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10890 Z= 0.094 Angle : 0.564 7.791 14830 Z= 0.285 Chirality : 0.043 0.167 1652 Planarity : 0.004 0.044 1882 Dihedral : 4.653 50.508 1463 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.44 % Allowed : 17.31 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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 are not related in a simple way. whole: -1.11 (0.23), residues: 1318 helix: -4.35 (0.55), residues: 40 sheet: 0.90 (0.23), residues: 514 loop : -1.82 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 457 TYR 0.011 0.001 TYR A 495 PHE 0.011 0.001 PHE I 170 TRP 0.012 0.001 TRP B 436 HIS 0.001 0.000 HIS L 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.09 (10870) covalent geometry : angle 0.56064 / 0.28 (14786) SS BOND : bond 0.00390 / 0.20 ( 16) SS BOND : angle 1.27899 / 0.80 ( 32) hydrogen bonds : bond 0.02773 / 1.91 ( 314) hydrogen bonds : angle 5.40390 / 3.69 ( 792) link_BETA1-4 : bond 0.00321 / 0.16 ( 2) link_BETA1-4 : angle 0.77572 / 0.59 ( 6) link_NAG-ASN : bond 0.00212 / 0.11 ( 2) link_NAG-ASN : angle 1.08686 / 0.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: H 142 LEU cc_start: 0.7564 (pp) cc_final: 0.7356 (pp) REVERT: L 31 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.7205 (t80) REVERT: L 149 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7521 (tm-30) REVERT: L 155 LYS cc_start: 0.7143 (mmmt) cc_final: 0.6842 (mmmt) REVERT: A 471 GLU cc_start: 0.4698 (OUTLIER) cc_final: 0.4398 (tp30) REVERT: B 471 GLU cc_start: 0.4885 (OUTLIER) cc_final: 0.4451 (tp30) REVERT: M 31 TYR cc_start: 0.8330 (OUTLIER) cc_final: 0.6430 (t80) REVERT: M 149 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7615 (tm-30) REVERT: M 155 LYS cc_start: 0.7113 (mmmt) cc_final: 0.6885 (mmmt) REVERT: I 2 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.6444 (ppp) REVERT: I 67 GLN cc_start: 0.8564 (mm-40) cc_final: 0.7767 (mt0) outliers start: 29 outliers final: 17 residues processed: 122 average time/residue: 0.1018 time to fit residues: 17.2288 Evaluate side-chains 117 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 181 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 184 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 70 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 44 optimal weight: 0.0570 chunk 9 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN A 493 GLN B 493 GLN M 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.137389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.122966 restraints weight = 16232.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.123562 restraints weight = 14170.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.123562 restraints weight = 12897.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.123562 restraints weight = 12896.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.123562 restraints weight = 12895.413| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10890 Z= 0.151 Angle : 0.598 8.140 14830 Z= 0.305 Chirality : 0.045 0.156 1652 Planarity : 0.004 0.043 1882 Dihedral : 4.751 48.845 1463 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.61 % Allowed : 16.55 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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 are not related in a simple way. whole: -1.16 (0.22), residues: 1318 helix: -4.38 (0.55), residues: 40 sheet: 0.81 (0.23), residues: 514 loop : -1.81 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.013 0.001 TYR H 180 PHE 0.015 0.002 PHE H 126 TRP 0.011 0.001 TRP B 436 HIS 0.002 0.001 HIS I 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 (10870) covalent geometry : angle 0.59463 / 0.30 (14786) SS BOND : bond 0.00573 / 0.31 ( 16) SS BOND : angle 1.42452 / 0.88 ( 32) hydrogen bonds : bond 0.03328 / 2.31 ( 314) hydrogen bonds : angle 5.45625 / 3.73 ( 792) link_BETA1-4 : bond 0.00295 / 0.15 ( 2) link_BETA1-4 : angle 1.03394 / 0.75 ( 6) link_NAG-ASN : bond 0.00068 / 0.03 ( 2) link_NAG-ASN : angle 1.29555 / 1.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 98 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: H 2 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.6474 (ppp) REVERT: H 67 GLN cc_start: 0.8677 (mm110) cc_final: 0.7631 (mt0) REVERT: H 142 LEU cc_start: 0.7621 (pp) cc_final: 0.7393 (pp) REVERT: L 31 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.6903 (t80) REVERT: L 149 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7660 (tm-30) REVERT: L 155 LYS cc_start: 0.7159 (mmmt) cc_final: 0.6847 (mmmt) REVERT: A 41 LYS cc_start: 0.7894 (tppt) cc_final: 0.6885 (mtmm) REVERT: A 471 GLU cc_start: 0.4844 (OUTLIER) cc_final: 0.4364 (tp30) REVERT: B 471 GLU cc_start: 0.4824 (OUTLIER) cc_final: 0.4346 (tp30) REVERT: M 31 TYR cc_start: 0.8401 (OUTLIER) cc_final: 0.6326 (t80) REVERT: M 51 LYS cc_start: 0.8218 (mttt) cc_final: 0.7727 (tttm) REVERT: M 149 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7739 (tm-30) REVERT: M 155 LYS cc_start: 0.7123 (mmmt) cc_final: 0.6889 (mmmt) REVERT: I 2 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.6551 (ppp) REVERT: I 67 GLN cc_start: 0.8569 (mm-40) cc_final: 0.7735 (mt0) REVERT: I 142 LEU cc_start: 0.7734 (pp) cc_final: 0.7500 (pp) outliers start: 43 outliers final: 36 residues processed: 135 average time/residue: 0.1073 time to fit residues: 20.4641 Evaluate side-chains 138 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 96 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 181 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 184 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 60 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 34 optimal weight: 0.0980 chunk 20 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN A 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.138467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.123984 restraints weight = 16381.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.124662 restraints weight = 14266.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.125405 restraints weight = 12883.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.125405 restraints weight = 11920.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.125405 restraints weight = 11920.034| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10890 Z= 0.137 Angle : 0.588 8.273 14830 Z= 0.299 Chirality : 0.044 0.163 1652 Planarity : 0.004 0.043 1882 Dihedral : 4.752 48.856 1463 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.70 % Allowed : 16.39 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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 are not related in a simple way. whole: -1.16 (0.22), residues: 1318 helix: -4.43 (0.53), residues: 40 sheet: 0.79 (0.23), residues: 514 loop : -1.79 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.012 0.001 TYR L 55 PHE 0.014 0.001 PHE H 126 TRP 0.011 0.001 TRP B 436 HIS 0.002 0.001 HIS I 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (10870) covalent geometry : angle 0.58504 / 0.30 (14786) SS BOND : bond 0.00545 / 0.29 ( 16) SS BOND : angle 1.36595 / 0.85 ( 32) hydrogen bonds : bond 0.03225 / 2.23 ( 314) hydrogen bonds : angle 5.45474 / 3.73 ( 792) link_BETA1-4 : bond 0.00304 / 0.15 ( 2) link_BETA1-4 : angle 0.96486 / 0.72 ( 6) link_NAG-ASN : bond 0.00089 / 0.04 ( 2) link_NAG-ASN : angle 1.27982 / 1.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 101 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: H 2 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.6496 (ppp) REVERT: H 67 GLN cc_start: 0.8663 (mm110) cc_final: 0.7624 (mt0) REVERT: H 142 LEU cc_start: 0.7602 (pp) cc_final: 0.7380 (pp) REVERT: L 31 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.6809 (t80) REVERT: L 149 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7647 (tm-30) REVERT: L 155 LYS cc_start: 0.7162 (mmmt) cc_final: 0.6877 (mmmt) REVERT: A 41 LYS cc_start: 0.7930 (tppt) cc_final: 0.6994 (mtmm) REVERT: A 471 GLU cc_start: 0.4936 (OUTLIER) cc_final: 0.4458 (tp30) REVERT: B 41 LYS cc_start: 0.7855 (tppt) cc_final: 0.6904 (mtmm) REVERT: B 471 GLU cc_start: 0.4804 (OUTLIER) cc_final: 0.4348 (tp30) REVERT: M 31 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.6292 (t80) REVERT: M 51 LYS cc_start: 0.8203 (mttt) cc_final: 0.7722 (tttm) REVERT: M 149 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7736 (tm-30) REVERT: M 155 LYS cc_start: 0.7101 (mmmt) cc_final: 0.6896 (mmmt) REVERT: I 2 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.6554 (ppp) REVERT: I 67 GLN cc_start: 0.8462 (mm-40) cc_final: 0.7628 (mt0) REVERT: I 133 LYS cc_start: 0.6588 (mttt) cc_final: 0.6309 (pttm) REVERT: I 142 LEU cc_start: 0.7714 (pp) cc_final: 0.7483 (pp) outliers start: 44 outliers final: 34 residues processed: 137 average time/residue: 0.1104 time to fit residues: 21.4058 Evaluate side-chains 141 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 101 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 181 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 201 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 65 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 74 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.0870 chunk 55 optimal weight: 0.0970 chunk 47 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN A 493 GLN B 474 GLN M 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.138856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.124387 restraints weight = 16202.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.124939 restraints weight = 14134.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.125710 restraints weight = 12875.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126020 restraints weight = 11953.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126020 restraints weight = 11320.177| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10890 Z= 0.111 Angle : 0.567 7.917 14830 Z= 0.288 Chirality : 0.044 0.160 1652 Planarity : 0.004 0.043 1882 Dihedral : 4.658 49.463 1463 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.36 % Allowed : 16.64 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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 are not related in a simple way. whole: -1.07 (0.22), residues: 1318 helix: -4.42 (0.52), residues: 40 sheet: 0.85 (0.23), residues: 514 loop : -1.72 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.012 0.001 TYR L 55 PHE 0.011 0.001 PHE H 126 TRP 0.012 0.001 TRP B 436 HIS 0.001 0.001 HIS I 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (10870) covalent geometry : angle 0.56420 / 0.29 (14786) SS BOND : bond 0.00499 / 0.26 ( 16) SS BOND : angle 1.24515 / 0.78 ( 32) hydrogen bonds : bond 0.03004 / 2.08 ( 314) hydrogen bonds : angle 5.35492 / 3.66 ( 792) link_BETA1-4 : bond 0.00333 / 0.16 ( 2) link_BETA1-4 : angle 0.91512 / 0.67 ( 6) link_NAG-ASN : bond 0.00133 / 0.07 ( 2) link_NAG-ASN : angle 1.21828 / 1.00 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 103 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: H 67 GLN cc_start: 0.8659 (mm110) cc_final: 0.7629 (mt0) REVERT: H 142 LEU cc_start: 0.7683 (pp) cc_final: 0.7457 (pp) REVERT: L 31 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.6675 (t80) REVERT: L 149 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7615 (tm-30) REVERT: L 155 LYS cc_start: 0.7127 (mmmt) cc_final: 0.6874 (mmmt) REVERT: A 471 GLU cc_start: 0.4896 (OUTLIER) cc_final: 0.4437 (tp30) REVERT: B 471 GLU cc_start: 0.4855 (OUTLIER) cc_final: 0.4404 (tp30) REVERT: M 31 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.6332 (t80) REVERT: M 51 LYS cc_start: 0.8183 (mttt) cc_final: 0.7700 (tttm) REVERT: M 149 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7696 (tm-30) REVERT: I 2 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.6537 (ppp) REVERT: I 67 GLN cc_start: 0.8461 (mm-40) cc_final: 0.7630 (mt0) REVERT: I 142 LEU cc_start: 0.7702 (pp) cc_final: 0.7473 (pp) outliers start: 40 outliers final: 33 residues processed: 137 average time/residue: 0.0951 time to fit residues: 18.6155 Evaluate side-chains 138 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 215 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain M residue 181 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 184 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 107 optimal weight: 0.4980 chunk 132 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 126 optimal weight: 0.0050 chunk 58 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN B 474 GLN M 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.138710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.122090 restraints weight = 16504.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.123859 restraints weight = 12411.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.125174 restraints weight = 9999.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.125998 restraints weight = 8529.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.126720 restraints weight = 7632.134| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10890 Z= 0.128 Angle : 0.580 7.950 14830 Z= 0.294 Chirality : 0.044 0.159 1652 Planarity : 0.004 0.043 1882 Dihedral : 4.667 49.167 1463 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.61 % Allowed : 16.72 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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 are not related in a simple way. whole: -1.07 (0.22), residues: 1318 helix: -4.41 (0.53), residues: 40 sheet: 0.84 (0.23), residues: 514 loop : -1.71 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.012 0.001 TYR L 55 PHE 0.013 0.001 PHE H 126 TRP 0.011 0.001 TRP B 436 HIS 0.002 0.001 HIS I 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (10870) covalent geometry : angle 0.57725 / 0.29 (14786) SS BOND : bond 0.00525 / 0.28 ( 16) SS BOND : angle 1.27924 / 0.80 ( 32) hydrogen bonds : bond 0.03118 / 2.16 ( 314) hydrogen bonds : angle 5.34255 / 3.65 ( 792) link_BETA1-4 : bond 0.00283 / 0.14 ( 2) link_BETA1-4 : angle 0.91777 / 0.67 ( 6) link_NAG-ASN : bond 0.00132 / 0.07 ( 2) link_NAG-ASN : angle 1.24882 / 1.02 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1656.86 seconds wall clock time: 29 minutes 29.42 seconds (1769.42 seconds total)