Starting phenix.real_space_refine on Sat Aug 23 10:03:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hm0_34887/08_2025/8hm0_34887.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hm0_34887/08_2025/8hm0_34887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hm0_34887/08_2025/8hm0_34887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hm0_34887/08_2025/8hm0_34887.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hm0_34887/08_2025/8hm0_34887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hm0_34887/08_2025/8hm0_34887.map" } resolution = 3.1 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= 0.000 sd= 0.003 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 60 5.16 5 C 7219 2.51 5 N 1915 2.21 5 O 2137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11331 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 1996 Classifications: {'peptide': 323} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 185} Link IDs: {'PTRANS': 6, 'TRANS': 316} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 675 Unresolved non-hydrogen angles: 854 Unresolved non-hydrogen dihedrals: 558 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'ASN:plan1': 12, 'PHE:plan': 14, 'GLN:plan1': 3, 'ASP:plan': 18, 'GLU:plan': 15, 'ARG:plan': 10, 'TRP:plan': 1, 'TYR:plan': 8, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 371 Chain: "A" Number of atoms: 7592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 935, 7592 Classifications: {'peptide': 935} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 31, 'TRANS': 900} Chain breaks: 3 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1743 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 3.49, per 1000 atoms: 0.31 Number of scatterers: 11331 At special positions: 0 Unit cell: (100.768, 121.136, 136.144, 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 60 16.00 O 2137 8.00 N 1915 7.00 C 7219 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 593.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2828 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 14 sheets defined 34.9% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'C' and resid 3 through 19 removed outlier: 3.628A pdb=" N ASN C 9 " --> pdb=" O ALA C 5 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER C 19 " --> pdb=" O SER C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 23 Processing helix chain 'C' and resid 24 through 43 removed outlier: 3.909A pdb=" N THR C 41 " --> pdb=" O TRP C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 121 removed outlier: 4.004A pdb=" N ALA C 113 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 159 removed outlier: 3.600A pdb=" N ILE C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 188 removed outlier: 4.685A pdb=" N MET C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.699A pdb=" N ASN C 321 " --> pdb=" O LYS C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 341 Processing helix chain 'C' and resid 343 through 350 removed outlier: 3.617A pdb=" N ASN C 350 " --> pdb=" O ARG C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 360 Processing helix chain 'C' and resid 367 through 373 Processing helix chain 'C' and resid 407 through 425 removed outlier: 3.615A pdb=" N THR C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 108 through 118 removed outlier: 3.607A pdb=" N ASN A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.736A pdb=" N PHE A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 240 through 253 Processing helix chain 'A' and resid 267 through 281 Processing helix chain 'A' and resid 330 through 339 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 389 Processing helix chain 'A' and resid 439 through 445 removed outlier: 3.737A pdb=" N LYS A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 473 removed outlier: 3.898A pdb=" N CYS A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP A 470 " --> pdb=" O CYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 486 removed outlier: 3.881A pdb=" N ASP A 480 " --> pdb=" O GLU A 476 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA A 484 " --> pdb=" O ASP A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 502 through 511 removed outlier: 3.544A pdb=" N LEU A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 561 Processing helix chain 'A' and resid 579 through 590 Processing helix chain 'A' and resid 621 through 643 Processing helix chain 'A' and resid 648 through 666 removed outlier: 3.724A pdb=" N ASP A 654 " --> pdb=" O LYS A 650 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 666 " --> pdb=" O ILE A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.797A pdb=" N GLY A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 701 removed outlier: 3.613A pdb=" N SER A 689 " --> pdb=" O LYS A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 776 removed outlier: 3.678A pdb=" N ARG A 776 " --> pdb=" O LYS A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 847 Processing helix chain 'A' and resid 859 through 883 removed outlier: 3.655A pdb=" N ARG A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 979 removed outlier: 3.898A pdb=" N THR A 976 " --> pdb=" O PHE A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 996 Processing helix chain 'B' and resid 19 through 38 removed outlier: 4.519A pdb=" N SER B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLN B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N SER B 35 " --> pdb=" O ASN B 31 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N TRP B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 55 Processing helix chain 'B' and resid 87 through 96 removed outlier: 3.589A pdb=" N GLU B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 150 removed outlier: 5.720A pdb=" N LYS B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ILE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 202 Processing sheet with id=AA1, first strand: chain 'C' and resid 130 through 132 Processing sheet with id=AA2, first strand: chain 'C' and resid 214 through 219 Processing sheet with id=AA3, first strand: chain 'C' and resid 226 through 229 removed outlier: 6.971A pdb=" N ILE C 232 " --> pdb=" O ILE C 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 375 through 380 removed outlier: 6.289A pdb=" N GLU C 380 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N VAL C 384 " --> pdb=" O GLU C 380 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 136 removed outlier: 7.043A pdb=" N CYS A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N TYR A 140 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE A 31 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE A 17 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG A 23 " --> pdb=" O CYS A 5 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N CYS A 5 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N CYS A 124 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 38 through 43 removed outlier: 6.278A pdb=" N SER A 84 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG A 64 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA A 86 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS A 62 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N MET A 88 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 72 through 73 removed outlier: 6.780A pdb=" N ILE A 614 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL A 571 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ILE A 612 " --> pdb=" O VAL A 571 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 166 through 169 removed outlier: 7.153A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 200 " --> pdb=" O TYR A 188 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU A 222 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AB1, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AB2, first strand: chain 'A' and resid 300 through 302 removed outlier: 3.523A pdb=" N THR A 317 " --> pdb=" O ARG A 302 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 355 through 364 removed outlier: 6.931A pdb=" N THR A 369 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ARG A 363 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLU A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A 407 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 745 through 748 removed outlier: 3.649A pdb=" N GLU A 758 " --> pdb=" O ARG A 746 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL A 748 " --> pdb=" O PHE A 756 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE A 756 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 548 " --> pdb=" O VAL A 755 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER A 812 " --> pdb=" O ALA A 793 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 116 through 119 removed outlier: 6.625A pdb=" N VAL B 62 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TRP B 119 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL B 64 " --> pdb=" O TRP B 119 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N CYS B 63 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LEU B 155 " --> pdb=" O ILE B 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 412 hydrogen bonds defined for protein. 1185 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: 1.90 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3691 1.34 - 1.46: 2284 1.46 - 1.58: 5489 1.58 - 1.69: 0 1.69 - 1.81: 89 Bond restraints: 11553 Sorted by residual: bond pdb=" C GLU B 20 " pdb=" N PRO B 21 " ideal model delta sigma weight residual 1.336 1.367 -0.031 1.08e-02 8.57e+03 8.26e+00 bond pdb=" CG LEU A 563 " pdb=" CD1 LEU A 563 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.63e+00 bond pdb=" CA ASP A 373 " pdb=" C ASP A 373 " ideal model delta sigma weight residual 1.523 1.508 0.015 1.21e-02 6.83e+03 1.54e+00 bond pdb=" CA SER A 708 " pdb=" C SER A 708 " ideal model delta sigma weight residual 1.532 1.521 0.012 9.60e-03 1.09e+04 1.45e+00 bond pdb=" N VAL B 64 " pdb=" CA VAL B 64 " ideal model delta sigma weight residual 1.474 1.456 0.018 1.57e-02 4.06e+03 1.35e+00 ... (remaining 11548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 15127 1.75 - 3.49: 461 3.49 - 5.24: 56 5.24 - 6.98: 14 6.98 - 8.73: 2 Bond angle restraints: 15660 Sorted by residual: angle pdb=" N THR C 41 " pdb=" CA THR C 41 " pdb=" C THR C 41 " ideal model delta sigma weight residual 114.56 109.83 4.73 1.27e+00 6.20e-01 1.39e+01 angle pdb=" N SER A 780 " pdb=" CA SER A 780 " pdb=" C SER A 780 " ideal model delta sigma weight residual 114.64 109.00 5.64 1.52e+00 4.33e-01 1.38e+01 angle pdb=" C ILE A 609 " pdb=" N SER A 610 " pdb=" CA SER A 610 " ideal model delta sigma weight residual 122.56 117.62 4.94 1.50e+00 4.44e-01 1.08e+01 angle pdb=" C PRO A 721 " pdb=" N PHE A 722 " pdb=" CA PHE A 722 " ideal model delta sigma weight residual 121.54 127.59 -6.05 1.91e+00 2.74e-01 1.00e+01 angle pdb=" N THR A 752 " pdb=" CA THR A 752 " pdb=" C THR A 752 " ideal model delta sigma weight residual 114.62 111.03 3.59 1.14e+00 7.69e-01 9.92e+00 ... (remaining 15655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6049 17.88 - 35.77: 701 35.77 - 53.65: 179 53.65 - 71.54: 39 71.54 - 89.42: 17 Dihedral angle restraints: 6985 sinusoidal: 2624 harmonic: 4361 Sorted by residual: dihedral pdb=" CA GLY A 434 " pdb=" C GLY A 434 " pdb=" N LYS A 435 " pdb=" CA LYS A 435 " ideal model delta harmonic sigma weight residual 180.00 151.72 28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA GLU C 365 " pdb=" C GLU C 365 " pdb=" N ALA C 366 " pdb=" CA ALA C 366 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA SER B 153 " pdb=" C SER B 153 " pdb=" N VAL B 154 " pdb=" CA VAL B 154 " ideal model delta harmonic sigma weight residual 180.00 154.12 25.88 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 6982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 972 0.031 - 0.062: 544 0.062 - 0.093: 177 0.093 - 0.125: 72 0.125 - 0.156: 15 Chirality restraints: 1780 Sorted by residual: chirality pdb=" CA ASP A 400 " pdb=" N ASP A 400 " pdb=" C ASP A 400 " pdb=" CB ASP A 400 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CB ILE A 739 " pdb=" CA ILE A 739 " pdb=" CG1 ILE A 739 " pdb=" CG2 ILE A 739 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CB VAL B 178 " pdb=" CA VAL B 178 " pdb=" CG1 VAL B 178 " pdb=" CG2 VAL B 178 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.55e-01 ... (remaining 1777 not shown) Planarity restraints: 2015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 554 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO A 555 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 555 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 555 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 593 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO A 594 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 594 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 594 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 564 " -0.028 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO A 565 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 565 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 565 " -0.023 5.00e-02 4.00e+02 ... (remaining 2012 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 558 2.71 - 3.26: 11439 3.26 - 3.80: 17513 3.80 - 4.35: 22258 4.35 - 4.90: 37335 Nonbonded interactions: 89103 Sorted by model distance: nonbonded pdb=" N ASP A 439 " pdb=" OD1 ASP A 439 " model vdw 2.162 3.120 nonbonded pdb=" O ALA C 5 " pdb=" OG1 THR C 8 " model vdw 2.213 3.040 nonbonded pdb=" O LYS A 973 " pdb=" OG SER A 977 " model vdw 2.220 3.040 nonbonded pdb=" NH1 ARG A 23 " pdb=" OG1 THR A 29 " model vdw 2.224 3.120 nonbonded pdb=" OE2 GLU A 205 " pdb=" NH1 ARG A 223 " model vdw 2.244 3.120 ... (remaining 89098 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.020 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11553 Z= 0.220 Angle : 0.724 8.729 15660 Z= 0.433 Chirality : 0.044 0.156 1780 Planarity : 0.004 0.045 2015 Dihedral : 17.210 89.420 4157 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.82 % Favored : 90.11 % Rotamer: Outliers : 9.92 % Allowed : 20.62 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.58 (0.18), residues: 1456 helix: -2.64 (0.18), residues: 498 sheet: -2.41 (0.33), residues: 212 loop : -3.60 (0.19), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 995 TYR 0.017 0.001 TYR A 486 PHE 0.013 0.001 PHE A 156 TRP 0.011 0.002 TRP A 89 HIS 0.002 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00481 (11553) covalent geometry : angle 0.72416 (15660) hydrogen bonds : bond 0.16319 ( 412) hydrogen bonds : angle 7.27628 ( 1185) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 162 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: C 355 ASP cc_start: 0.6552 (t0) cc_final: 0.5863 (t0) REVERT: C 359 GLU cc_start: 0.7765 (tt0) cc_final: 0.6783 (mt-10) REVERT: C 365 GLU cc_start: 0.7494 (mp0) cc_final: 0.6790 (mp0) REVERT: C 369 ILE cc_start: 0.6735 (pt) cc_final: 0.6371 (pt) REVERT: C 374 ASN cc_start: 0.7222 (m-40) cc_final: 0.6889 (m110) REVERT: C 376 ARG cc_start: 0.6567 (mmm160) cc_final: 0.6098 (mmm160) REVERT: A 152 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7193 (tt0) REVERT: A 357 MET cc_start: 0.7372 (mmm) cc_final: 0.6645 (mpp) REVERT: A 426 ASN cc_start: 0.8226 (t0) cc_final: 0.8007 (t0) REVERT: A 435 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7123 (tppt) REVERT: A 436 ASP cc_start: 0.6814 (OUTLIER) cc_final: 0.6380 (t0) REVERT: A 497 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7050 (mtm180) REVERT: A 576 ASN cc_start: 0.7519 (m110) cc_final: 0.7309 (m-40) REVERT: A 711 MET cc_start: 0.4115 (ttt) cc_final: 0.3740 (tmm) REVERT: A 769 GLU cc_start: 0.7733 (tp30) cc_final: 0.7388 (mp0) outliers start: 116 outliers final: 85 residues processed: 266 average time/residue: 0.1003 time to fit residues: 38.1385 Evaluate side-chains 230 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 141 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 TYR Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 784 PHE Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN A 524 GLN A 562 ASN A 730 ASN A 860 ASN A 994 GLN B 25 GLN B 55 GLN B 59 ASN B 111 ASN B 146 GLN B 188 GLN B 214 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.179521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.124112 restraints weight = 16990.685| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.50 r_work: 0.3552 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11553 Z= 0.147 Angle : 0.612 8.432 15660 Z= 0.329 Chirality : 0.044 0.188 1780 Planarity : 0.004 0.048 2015 Dihedral : 9.894 60.190 1749 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 7.53 % Allowed : 21.73 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.30 (0.20), residues: 1456 helix: -1.26 (0.21), residues: 514 sheet: -1.98 (0.33), residues: 214 loop : -3.01 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 713 TYR 0.014 0.001 TYR A 486 PHE 0.030 0.001 PHE C 410 TRP 0.009 0.001 TRP A 470 HIS 0.002 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00330 (11553) covalent geometry : angle 0.61206 (15660) hydrogen bonds : bond 0.04466 ( 412) hydrogen bonds : angle 5.35182 ( 1185) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 157 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: C 355 ASP cc_start: 0.7208 (t0) cc_final: 0.6847 (t0) REVERT: C 359 GLU cc_start: 0.8018 (tt0) cc_final: 0.7300 (mt-10) REVERT: C 365 GLU cc_start: 0.7708 (mp0) cc_final: 0.7121 (mp0) REVERT: C 374 ASN cc_start: 0.7503 (m-40) cc_final: 0.7109 (m110) REVERT: C 376 ARG cc_start: 0.6884 (mmm160) cc_final: 0.6480 (mmm160) REVERT: A 36 HIS cc_start: 0.8830 (OUTLIER) cc_final: 0.8596 (t70) REVERT: A 129 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7783 (pm20) REVERT: A 143 ASP cc_start: 0.7473 (p0) cc_final: 0.7191 (p0) REVERT: A 299 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.9042 (mm) REVERT: A 357 MET cc_start: 0.7254 (mmm) cc_final: 0.6623 (mpp) REVERT: A 508 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8075 (mtmt) REVERT: A 576 ASN cc_start: 0.8070 (m110) cc_final: 0.7689 (m110) REVERT: B 38 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8936 (mt) REVERT: B 65 CYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8106 (m) REVERT: B 129 GLU cc_start: 0.7356 (mp0) cc_final: 0.7120 (mp0) outliers start: 88 outliers final: 56 residues processed: 228 average time/residue: 0.1078 time to fit residues: 35.3088 Evaluate side-chains 202 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 141 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 36 HIS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 TYR Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 784 PHE Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 135 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.176617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.120769 restraints weight = 17050.416| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.49 r_work: 0.3504 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11553 Z= 0.244 Angle : 0.651 7.078 15660 Z= 0.347 Chirality : 0.046 0.172 1780 Planarity : 0.005 0.043 2015 Dihedral : 8.992 59.581 1672 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 7.78 % Allowed : 22.58 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.01 (0.20), residues: 1456 helix: -1.08 (0.21), residues: 529 sheet: -1.78 (0.34), residues: 208 loop : -2.81 (0.21), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 713 TYR 0.020 0.002 TYR A 486 PHE 0.036 0.002 PHE C 410 TRP 0.011 0.002 TRP A 470 HIS 0.002 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00581 (11553) covalent geometry : angle 0.65120 (15660) hydrogen bonds : bond 0.04864 ( 412) hydrogen bonds : angle 5.27713 ( 1185) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 141 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 355 ASP cc_start: 0.7403 (t0) cc_final: 0.7029 (t0) REVERT: C 359 GLU cc_start: 0.8106 (tt0) cc_final: 0.7356 (mt-10) REVERT: C 365 GLU cc_start: 0.7758 (mp0) cc_final: 0.7532 (mm-30) REVERT: C 371 LEU cc_start: 0.6559 (tp) cc_final: 0.6169 (tt) REVERT: C 374 ASN cc_start: 0.7305 (m-40) cc_final: 0.6917 (m110) REVERT: C 376 ARG cc_start: 0.6964 (mmm160) cc_final: 0.6523 (mmm160) REVERT: C 424 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7898 (tp) REVERT: A 36 HIS cc_start: 0.8859 (OUTLIER) cc_final: 0.8619 (t70) REVERT: A 129 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7796 (pm20) REVERT: A 143 ASP cc_start: 0.7392 (p0) cc_final: 0.7180 (p0) REVERT: A 299 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9120 (mm) REVERT: A 357 MET cc_start: 0.7330 (mmm) cc_final: 0.6318 (mpp) REVERT: A 426 ASN cc_start: 0.8436 (t0) cc_final: 0.8177 (t0) REVERT: A 497 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7138 (mtm180) REVERT: A 711 MET cc_start: 0.4644 (ttt) cc_final: 0.3932 (tmm) REVERT: A 769 GLU cc_start: 0.8193 (tp30) cc_final: 0.7534 (mp0) REVERT: B 65 CYS cc_start: 0.8444 (m) cc_final: 0.8106 (m) REVERT: B 189 PHE cc_start: 0.6641 (OUTLIER) cc_final: 0.5740 (m-10) outliers start: 91 outliers final: 70 residues processed: 219 average time/residue: 0.1058 time to fit residues: 33.8319 Evaluate side-chains 213 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 138 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 36 HIS Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 TYR Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 784 PHE Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 63 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 61 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 111 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 132 optimal weight: 0.0470 chunk 57 optimal weight: 0.9990 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.178946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.125391 restraints weight = 17048.595| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.42 r_work: 0.3530 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11553 Z= 0.117 Angle : 0.570 8.770 15660 Z= 0.304 Chirality : 0.043 0.176 1780 Planarity : 0.004 0.038 2015 Dihedral : 8.161 59.774 1664 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 6.50 % Allowed : 24.21 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.44 (0.21), residues: 1456 helix: -0.44 (0.23), residues: 509 sheet: -1.73 (0.33), residues: 229 loop : -2.51 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 713 TYR 0.013 0.001 TYR A 486 PHE 0.031 0.001 PHE C 410 TRP 0.009 0.001 TRP A 8 HIS 0.002 0.000 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00259 (11553) covalent geometry : angle 0.57026 (15660) hydrogen bonds : bond 0.03703 ( 412) hydrogen bonds : angle 4.91446 ( 1185) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 165 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 355 ASP cc_start: 0.7310 (t0) cc_final: 0.6824 (t0) REVERT: C 359 GLU cc_start: 0.8275 (tt0) cc_final: 0.7394 (mt-10) REVERT: C 365 GLU cc_start: 0.7761 (mp0) cc_final: 0.7470 (mm-30) REVERT: C 374 ASN cc_start: 0.7252 (m-40) cc_final: 0.6837 (m110) REVERT: C 378 LYS cc_start: 0.7815 (ttmt) cc_final: 0.7356 (mttm) REVERT: A 36 HIS cc_start: 0.8791 (OUTLIER) cc_final: 0.8552 (t70) REVERT: A 129 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7585 (pm20) REVERT: A 192 ASP cc_start: 0.8547 (t0) cc_final: 0.8263 (t0) REVERT: A 299 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.9014 (mm) REVERT: A 350 SER cc_start: 0.8842 (t) cc_final: 0.8274 (p) REVERT: A 357 MET cc_start: 0.7203 (mmm) cc_final: 0.6546 (mpp) REVERT: A 426 ASN cc_start: 0.8380 (t0) cc_final: 0.7909 (t0) REVERT: A 972 PHE cc_start: 0.5993 (OUTLIER) cc_final: 0.5578 (t80) REVERT: B 129 GLU cc_start: 0.7441 (mp0) cc_final: 0.7210 (mp0) REVERT: B 185 ARG cc_start: 0.6353 (mpp-170) cc_final: 0.6147 (mpp-170) outliers start: 76 outliers final: 55 residues processed: 225 average time/residue: 0.0955 time to fit residues: 31.6582 Evaluate side-chains 203 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 145 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain A residue 36 HIS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 TYR Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 784 PHE Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 160 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 ASN B 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.177239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.121302 restraints weight = 17050.124| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.48 r_work: 0.3520 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11553 Z= 0.227 Angle : 0.625 8.637 15660 Z= 0.332 Chirality : 0.046 0.145 1780 Planarity : 0.004 0.040 2015 Dihedral : 8.155 59.040 1653 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 7.53 % Allowed : 23.70 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.45 (0.21), residues: 1456 helix: -0.56 (0.22), residues: 523 sheet: -1.45 (0.35), residues: 208 loop : -2.54 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 692 TYR 0.019 0.002 TYR A 486 PHE 0.030 0.002 PHE A 791 TRP 0.009 0.002 TRP A 470 HIS 0.002 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00539 (11553) covalent geometry : angle 0.62545 (15660) hydrogen bonds : bond 0.04424 ( 412) hydrogen bonds : angle 5.02549 ( 1185) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 148 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 322 LYS cc_start: 0.7542 (mmtt) cc_final: 0.6849 (mmtp) REVERT: C 355 ASP cc_start: 0.7418 (t0) cc_final: 0.7152 (t0) REVERT: C 359 GLU cc_start: 0.8163 (tt0) cc_final: 0.7565 (mt-10) REVERT: C 365 GLU cc_start: 0.7760 (mp0) cc_final: 0.7491 (mm-30) REVERT: C 374 ASN cc_start: 0.7246 (m-40) cc_final: 0.6844 (m110) REVERT: C 378 LYS cc_start: 0.7735 (ttmt) cc_final: 0.7282 (mttm) REVERT: C 379 ILE cc_start: 0.8383 (mt) cc_final: 0.8130 (mp) REVERT: A 36 HIS cc_start: 0.8864 (OUTLIER) cc_final: 0.8604 (t70) REVERT: A 129 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7571 (pm20) REVERT: A 233 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8749 (mt-10) REVERT: A 299 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.9121 (mm) REVERT: A 357 MET cc_start: 0.7313 (mmm) cc_final: 0.6315 (mpp) REVERT: A 426 ASN cc_start: 0.8410 (t0) cc_final: 0.7966 (t0) REVERT: A 497 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7229 (mtm180) REVERT: A 711 MET cc_start: 0.4698 (tmm) cc_final: 0.4400 (tmm) REVERT: A 713 ARG cc_start: 0.8286 (ptm-80) cc_final: 0.8082 (ptm-80) REVERT: A 972 PHE cc_start: 0.6111 (OUTLIER) cc_final: 0.5536 (t80) REVERT: B 189 PHE cc_start: 0.6657 (OUTLIER) cc_final: 0.5830 (m-10) outliers start: 88 outliers final: 66 residues processed: 223 average time/residue: 0.0989 time to fit residues: 32.2005 Evaluate side-chains 216 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 144 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 32 ASN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 36 HIS Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 TYR Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 784 PHE Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 63 optimal weight: 0.6980 chunk 106 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 52 optimal weight: 0.6980 chunk 127 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.180878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.124693 restraints weight = 16879.068| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.53 r_work: 0.3564 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11553 Z= 0.122 Angle : 0.565 8.435 15660 Z= 0.302 Chirality : 0.044 0.213 1780 Planarity : 0.004 0.038 2015 Dihedral : 7.658 59.161 1650 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 6.33 % Allowed : 24.29 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.02 (0.21), residues: 1456 helix: -0.13 (0.23), residues: 511 sheet: -1.27 (0.35), residues: 208 loop : -2.30 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 692 TYR 0.013 0.001 TYR A 486 PHE 0.030 0.001 PHE A 791 TRP 0.009 0.001 TRP A 470 HIS 0.002 0.000 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00277 (11553) covalent geometry : angle 0.56460 (15660) hydrogen bonds : bond 0.03636 ( 412) hydrogen bonds : angle 4.78380 ( 1185) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 160 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 355 ASP cc_start: 0.7313 (t0) cc_final: 0.7062 (t0) REVERT: C 359 GLU cc_start: 0.8156 (tt0) cc_final: 0.7504 (mt-10) REVERT: C 365 GLU cc_start: 0.7709 (mp0) cc_final: 0.7428 (mm-30) REVERT: C 374 ASN cc_start: 0.7280 (m-40) cc_final: 0.7063 (m110) REVERT: C 378 LYS cc_start: 0.7694 (ttmt) cc_final: 0.7259 (mtmm) REVERT: A 129 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7546 (pm20) REVERT: A 143 ASP cc_start: 0.7017 (p0) cc_final: 0.6530 (p0) REVERT: A 192 ASP cc_start: 0.8552 (t0) cc_final: 0.8294 (t0) REVERT: A 299 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.9038 (mm) REVERT: A 357 MET cc_start: 0.7287 (mmm) cc_final: 0.6611 (mpp) REVERT: A 426 ASN cc_start: 0.8393 (t0) cc_final: 0.7977 (t0) REVERT: A 508 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7864 (mtmt) REVERT: A 713 ARG cc_start: 0.8225 (ptm-80) cc_final: 0.7997 (ptm-80) REVERT: A 784 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7934 (p90) REVERT: A 972 PHE cc_start: 0.6055 (OUTLIER) cc_final: 0.5620 (t80) outliers start: 74 outliers final: 57 residues processed: 222 average time/residue: 0.1050 time to fit residues: 33.5016 Evaluate side-chains 214 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 153 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 TYR Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 784 PHE Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 160 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 109 optimal weight: 0.0670 chunk 75 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.179909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.124574 restraints weight = 16873.174| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.51 r_work: 0.3500 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11553 Z= 0.117 Angle : 0.564 8.435 15660 Z= 0.299 Chirality : 0.043 0.153 1780 Planarity : 0.004 0.039 2015 Dihedral : 7.399 59.616 1647 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 5.73 % Allowed : 25.15 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.22), residues: 1456 helix: 0.03 (0.23), residues: 513 sheet: -1.13 (0.35), residues: 208 loop : -2.20 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 692 TYR 0.012 0.001 TYR A 486 PHE 0.037 0.001 PHE A 791 TRP 0.009 0.001 TRP A 8 HIS 0.003 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00264 (11553) covalent geometry : angle 0.56385 (15660) hydrogen bonds : bond 0.03549 ( 412) hydrogen bonds : angle 4.70025 ( 1185) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 164 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 322 LYS cc_start: 0.7469 (mmtt) cc_final: 0.6533 (mmtm) REVERT: C 355 ASP cc_start: 0.7257 (t0) cc_final: 0.6798 (t0) REVERT: C 359 GLU cc_start: 0.8228 (tt0) cc_final: 0.7494 (mt-10) REVERT: C 365 GLU cc_start: 0.7741 (mp0) cc_final: 0.7458 (mm-30) REVERT: C 378 LYS cc_start: 0.7691 (ttmt) cc_final: 0.7064 (mttm) REVERT: A 129 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7471 (pm20) REVERT: A 143 ASP cc_start: 0.7098 (p0) cc_final: 0.6629 (p0) REVERT: A 192 ASP cc_start: 0.8560 (t0) cc_final: 0.8308 (t0) REVERT: A 299 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.9065 (mm) REVERT: A 350 SER cc_start: 0.8845 (t) cc_final: 0.8276 (p) REVERT: A 357 MET cc_start: 0.7211 (mmm) cc_final: 0.6513 (mpp) REVERT: A 426 ASN cc_start: 0.8425 (t0) cc_final: 0.8001 (t0) REVERT: A 508 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7980 (mtmt) REVERT: A 972 PHE cc_start: 0.6036 (OUTLIER) cc_final: 0.5594 (t80) REVERT: B 28 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7611 (pp20) REVERT: B 189 PHE cc_start: 0.6944 (OUTLIER) cc_final: 0.6097 (m-10) outliers start: 67 outliers final: 57 residues processed: 220 average time/residue: 0.1013 time to fit residues: 31.8837 Evaluate side-chains 223 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 161 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 TYR Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 784 PHE Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 189 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 112 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 0.0170 chunk 69 optimal weight: 5.9990 chunk 129 optimal weight: 0.1980 chunk 6 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 overall best weight: 0.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 373 ASN ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.181218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.125030 restraints weight = 16960.277| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.53 r_work: 0.3516 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11553 Z= 0.127 Angle : 0.570 7.889 15660 Z= 0.302 Chirality : 0.044 0.149 1780 Planarity : 0.004 0.036 2015 Dihedral : 7.319 58.974 1646 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 5.99 % Allowed : 25.32 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.22), residues: 1456 helix: 0.12 (0.23), residues: 517 sheet: -1.05 (0.36), residues: 208 loop : -2.14 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 692 TYR 0.013 0.001 TYR A 486 PHE 0.033 0.001 PHE A 791 TRP 0.009 0.001 TRP A 8 HIS 0.006 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00291 (11553) covalent geometry : angle 0.56983 (15660) hydrogen bonds : bond 0.03608 ( 412) hydrogen bonds : angle 4.65753 ( 1185) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 160 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 22 PHE cc_start: 0.5927 (m-80) cc_final: 0.5597 (m-80) REVERT: C 322 LYS cc_start: 0.7203 (mmtt) cc_final: 0.6568 (mmtm) REVERT: C 347 LYS cc_start: 0.8399 (tmtt) cc_final: 0.7230 (mttt) REVERT: C 355 ASP cc_start: 0.7397 (t0) cc_final: 0.7060 (t0) REVERT: C 359 GLU cc_start: 0.8143 (tt0) cc_final: 0.7488 (mt-10) REVERT: C 365 GLU cc_start: 0.7803 (mp0) cc_final: 0.7511 (mm-30) REVERT: A 129 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7507 (pm20) REVERT: A 143 ASP cc_start: 0.7079 (p0) cc_final: 0.6623 (p0) REVERT: A 192 ASP cc_start: 0.8571 (t0) cc_final: 0.8314 (t0) REVERT: A 233 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8734 (mt-10) REVERT: A 299 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9076 (mm) REVERT: A 357 MET cc_start: 0.7059 (mmm) cc_final: 0.6444 (mpp) REVERT: A 426 ASN cc_start: 0.8411 (t0) cc_final: 0.8062 (t0) REVERT: A 784 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7862 (p90) REVERT: A 972 PHE cc_start: 0.6024 (OUTLIER) cc_final: 0.5578 (t80) REVERT: B 28 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7551 (pp20) REVERT: B 86 LYS cc_start: 0.6391 (mmtt) cc_final: 0.6032 (mmtt) REVERT: B 189 PHE cc_start: 0.6881 (OUTLIER) cc_final: 0.6034 (m-10) outliers start: 70 outliers final: 54 residues processed: 221 average time/residue: 0.1047 time to fit residues: 33.1164 Evaluate side-chains 208 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 148 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 TYR Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 784 PHE Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 189 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 71 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 30.0000 chunk 57 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 135 optimal weight: 0.0010 chunk 118 optimal weight: 7.9990 chunk 81 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.181692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.126009 restraints weight = 16856.807| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.53 r_work: 0.3579 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11553 Z= 0.121 Angle : 0.584 10.115 15660 Z= 0.309 Chirality : 0.044 0.302 1780 Planarity : 0.004 0.036 2015 Dihedral : 7.229 59.598 1644 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 5.73 % Allowed : 25.41 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.22), residues: 1456 helix: 0.16 (0.23), residues: 520 sheet: -0.97 (0.36), residues: 205 loop : -2.07 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 692 TYR 0.012 0.001 TYR A 486 PHE 0.029 0.001 PHE A 791 TRP 0.009 0.001 TRP A 8 HIS 0.005 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00275 (11553) covalent geometry : angle 0.58443 (15660) hydrogen bonds : bond 0.03511 ( 412) hydrogen bonds : angle 4.61857 ( 1185) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 155 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 22 PHE cc_start: 0.6002 (m-80) cc_final: 0.5678 (m-80) REVERT: C 318 GLN cc_start: 0.8243 (pm20) cc_final: 0.8019 (pm20) REVERT: C 322 LYS cc_start: 0.7132 (mmtt) cc_final: 0.6593 (mmtm) REVERT: C 347 LYS cc_start: 0.8414 (tmtt) cc_final: 0.7248 (mttt) REVERT: C 355 ASP cc_start: 0.7467 (t0) cc_final: 0.7140 (t0) REVERT: C 359 GLU cc_start: 0.8225 (tt0) cc_final: 0.7620 (mt-10) REVERT: C 365 GLU cc_start: 0.7837 (mp0) cc_final: 0.7579 (mm-30) REVERT: C 378 LYS cc_start: 0.7827 (ttmt) cc_final: 0.7148 (mtmm) REVERT: A 129 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7518 (pm20) REVERT: A 143 ASP cc_start: 0.7044 (p0) cc_final: 0.6560 (p0) REVERT: A 192 ASP cc_start: 0.8535 (t0) cc_final: 0.8303 (t0) REVERT: A 233 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8721 (mt-10) REVERT: A 299 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.9061 (mm) REVERT: A 350 SER cc_start: 0.8851 (t) cc_final: 0.8285 (p) REVERT: A 357 MET cc_start: 0.7034 (mmm) cc_final: 0.6446 (mpp) REVERT: A 508 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7806 (mtmt) REVERT: A 972 PHE cc_start: 0.6037 (OUTLIER) cc_final: 0.5590 (t80) REVERT: B 28 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7510 (pp20) REVERT: B 189 PHE cc_start: 0.6910 (OUTLIER) cc_final: 0.6069 (m-10) outliers start: 67 outliers final: 56 residues processed: 212 average time/residue: 0.1026 time to fit residues: 31.5191 Evaluate side-chains 212 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 150 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 TYR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 784 PHE Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 189 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 145 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 10 optimal weight: 0.0980 chunk 94 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 ASN ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.180177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.124216 restraints weight = 17037.797| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.52 r_work: 0.3553 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11553 Z= 0.170 Angle : 0.610 8.740 15660 Z= 0.323 Chirality : 0.045 0.345 1780 Planarity : 0.004 0.061 2015 Dihedral : 7.279 59.798 1641 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 5.90 % Allowed : 25.58 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.22), residues: 1456 helix: 0.08 (0.23), residues: 518 sheet: -1.14 (0.35), residues: 218 loop : -2.09 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 692 TYR 0.016 0.001 TYR A 486 PHE 0.029 0.002 PHE A 791 TRP 0.008 0.001 TRP A 470 HIS 0.007 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00402 (11553) covalent geometry : angle 0.61032 (15660) hydrogen bonds : bond 0.03888 ( 412) hydrogen bonds : angle 4.69721 ( 1185) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 148 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 22 PHE cc_start: 0.6046 (m-80) cc_final: 0.5722 (m-80) REVERT: C 322 LYS cc_start: 0.7008 (mmtt) cc_final: 0.6483 (mmtm) REVERT: C 347 LYS cc_start: 0.8422 (tmtt) cc_final: 0.7231 (mttt) REVERT: C 355 ASP cc_start: 0.7473 (t0) cc_final: 0.7101 (t0) REVERT: C 359 GLU cc_start: 0.8210 (tt0) cc_final: 0.7572 (mt-10) REVERT: C 365 GLU cc_start: 0.7865 (mp0) cc_final: 0.7576 (mm-30) REVERT: C 376 ARG cc_start: 0.7622 (tpp-160) cc_final: 0.6976 (mmm160) REVERT: C 378 LYS cc_start: 0.7742 (ttmt) cc_final: 0.7027 (mtmm) REVERT: A 129 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7544 (pm20) REVERT: A 143 ASP cc_start: 0.7021 (p0) cc_final: 0.6502 (p0) REVERT: A 233 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8719 (mt-10) REVERT: A 299 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9083 (mm) REVERT: A 357 MET cc_start: 0.7095 (mmm) cc_final: 0.6257 (mpp) REVERT: A 426 ASN cc_start: 0.8427 (t0) cc_final: 0.8057 (t0) REVERT: A 508 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7816 (mtmt) REVERT: A 546 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7864 (mm) REVERT: A 972 PHE cc_start: 0.6065 (OUTLIER) cc_final: 0.5563 (t80) REVERT: B 28 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7543 (pp20) REVERT: B 189 PHE cc_start: 0.6919 (OUTLIER) cc_final: 0.6062 (m-10) outliers start: 69 outliers final: 57 residues processed: 207 average time/residue: 0.1095 time to fit residues: 32.6954 Evaluate side-chains 211 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 147 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 TYR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 784 PHE Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 189 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 62 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 76 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 115 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.181469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.125561 restraints weight = 16927.200| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.53 r_work: 0.3503 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11553 Z= 0.132 Angle : 0.589 8.125 15660 Z= 0.312 Chirality : 0.045 0.400 1780 Planarity : 0.004 0.052 2015 Dihedral : 7.171 59.542 1641 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 5.73 % Allowed : 25.83 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.22), residues: 1456 helix: 0.18 (0.23), residues: 517 sheet: -1.06 (0.35), residues: 217 loop : -2.03 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 692 TYR 0.013 0.001 TYR A 486 PHE 0.027 0.001 PHE A 791 TRP 0.009 0.001 TRP A 8 HIS 0.005 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00304 (11553) covalent geometry : angle 0.58878 (15660) hydrogen bonds : bond 0.03627 ( 412) hydrogen bonds : angle 4.63428 ( 1185) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4390.30 seconds wall clock time: 75 minutes 33.49 seconds (4533.49 seconds total)