Starting phenix.real_space_refine on Sun Dec 29 20:36:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hm0_34887/12_2024/8hm0_34887.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hm0_34887/12_2024/8hm0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hm0_34887/12_2024/8hm0_34887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hm0_34887/12_2024/8hm0_34887.map" model { file = "/net/cci-nas-00/data/ceres_data/8hm0_34887/12_2024/8hm0_34887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hm0_34887/12_2024/8hm0_34887.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 8, 'ASN:plan1': 12, 'TRP:plan': 1, 'ASP:plan': 18, 'PHE:plan': 14, 'GLU:plan': 15, 'ARG:plan': 10} 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, 'PHE:plan': 1, 'ASN:plan1': 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: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 6.80, per 1000 atoms: 0.60 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: 2.71 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.31 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: 3.78 Time building geometry restraints manager: 3.19 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: 0.010 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 27.640 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.030 ------------------------------------------------------------------------------- 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= 0.309 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.002 TRP A 89 HIS 0.002 0.001 HIS A 319 PHE 0.013 0.001 PHE A 156 TYR 0.017 0.001 TYR A 486 ARG 0.004 0.000 ARG A 995 *********************** 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 : 1.458 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: 0.2623 time to fit residues: 99.6727 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 : 1.218 ------------------------------------------------------------------------------- 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 123 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 37 optimal weight: 0.0030 chunk 74 optimal weight: 0.0370 chunk 59 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 69 optimal weight: 0.0050 chunk 85 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.2482 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1344 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= 0.167 Angle : 0.596 8.311 15660 Z= 0.321 Chirality : 0.043 0.186 1780 Planarity : 0.004 0.046 2015 Dihedral : 9.551 58.988 1749 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 6.76 % Allowed : 21.90 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.20), residues: 1456 helix: -1.12 (0.22), residues: 508 sheet: -1.98 (0.33), residues: 214 loop : -2.93 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 43 HIS 0.003 0.001 HIS A 185 PHE 0.027 0.001 PHE C 410 TYR 0.012 0.001 TYR C 404 ARG 0.009 0.000 ARG A 713 *********************** 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 243 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 164 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 355 ASP cc_start: 0.6782 (t0) cc_final: 0.6264 (t0) REVERT: C 359 GLU cc_start: 0.7744 (tt0) cc_final: 0.6993 (mt-10) REVERT: C 365 GLU cc_start: 0.7423 (mp0) cc_final: 0.6938 (mp0) REVERT: C 374 ASN cc_start: 0.6973 (m-40) cc_final: 0.6697 (m110) REVERT: C 376 ARG cc_start: 0.6813 (mmm160) cc_final: 0.6519 (mmm160) REVERT: A 36 HIS cc_start: 0.8363 (OUTLIER) cc_final: 0.8125 (t70) REVERT: A 299 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8764 (mm) REVERT: A 350 SER cc_start: 0.8604 (t) cc_final: 0.8202 (p) REVERT: A 357 MET cc_start: 0.7164 (mmm) cc_final: 0.6556 (mpp) REVERT: A 508 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7795 (mtmt) REVERT: A 576 ASN cc_start: 0.7341 (m110) cc_final: 0.7002 (m110) REVERT: A 712 LEU cc_start: 0.5912 (pt) cc_final: 0.5659 (tp) REVERT: B 65 CYS cc_start: 0.8103 (m) cc_final: 0.7735 (m) outliers start: 79 outliers final: 50 residues processed: 229 average time/residue: 0.2478 time to fit residues: 80.5581 Evaluate side-chains 198 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 145 time to evaluate : 1.375 ------------------------------------------------------------------------------- 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 230 MET Chi-restraints excluded: chain A residue 280 THR 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 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 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 830 GLU Chi-restraints excluded: chain A residue 839 HIS 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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** B 188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1523 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= 0.259 Angle : 0.593 6.937 15660 Z= 0.317 Chirality : 0.044 0.155 1780 Planarity : 0.004 0.050 2015 Dihedral : 8.421 59.010 1664 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 7.61 % Allowed : 22.41 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.21), residues: 1456 helix: -0.80 (0.22), residues: 522 sheet: -1.88 (0.33), residues: 218 loop : -2.71 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 470 HIS 0.002 0.000 HIS A 461 PHE 0.034 0.002 PHE C 410 TYR 0.016 0.001 TYR A 486 ARG 0.008 0.000 ARG A 713 *********************** 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 235 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 146 time to evaluate : 1.263 Fit side-chains revert: symmetry clash REVERT: C 347 LYS cc_start: 0.8557 (tmtt) cc_final: 0.8216 (tptp) REVERT: C 355 ASP cc_start: 0.6893 (t0) cc_final: 0.6457 (t0) REVERT: C 359 GLU cc_start: 0.7873 (tt0) cc_final: 0.7116 (mt-10) REVERT: C 365 GLU cc_start: 0.7567 (mp0) cc_final: 0.7324 (mm-30) REVERT: C 374 ASN cc_start: 0.6923 (m-40) cc_final: 0.6619 (m110) REVERT: A 36 HIS cc_start: 0.8391 (OUTLIER) cc_final: 0.8115 (t70) REVERT: A 299 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8841 (mm) REVERT: A 357 MET cc_start: 0.7203 (mmm) cc_final: 0.6630 (mpp) REVERT: A 426 ASN cc_start: 0.8377 (t0) cc_final: 0.8149 (t0) REVERT: A 972 PHE cc_start: 0.6469 (OUTLIER) cc_final: 0.5760 (t80) REVERT: B 65 CYS cc_start: 0.8067 (m) cc_final: 0.7724 (m) outliers start: 89 outliers final: 63 residues processed: 220 average time/residue: 0.2394 time to fit residues: 76.9933 Evaluate side-chains 205 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 139 time to evaluate : 1.318 ------------------------------------------------------------------------------- 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 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 183 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 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 365 VAL Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 411 LEU 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 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 763 ASP 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 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 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 165 ASN 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 131 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1787 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= 0.210 Angle : 0.579 7.858 15660 Z= 0.307 Chirality : 0.044 0.165 1780 Planarity : 0.004 0.037 2015 Dihedral : 7.987 59.933 1658 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 6.93 % Allowed : 23.10 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.21), residues: 1456 helix: -0.48 (0.22), residues: 521 sheet: -1.77 (0.33), residues: 229 loop : -2.52 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.002 0.000 HIS A 461 PHE 0.028 0.001 PHE C 410 TYR 0.015 0.001 TYR A 486 ARG 0.008 0.000 ARG A 713 *********************** 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 239 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 158 time to evaluate : 1.292 Fit side-chains revert: symmetry clash REVERT: C 355 ASP cc_start: 0.6895 (t0) cc_final: 0.6502 (t0) REVERT: C 359 GLU cc_start: 0.7924 (tt0) cc_final: 0.7163 (mt-10) REVERT: C 365 GLU cc_start: 0.7532 (mp0) cc_final: 0.7294 (mm-30) REVERT: C 374 ASN cc_start: 0.6953 (m-40) cc_final: 0.6616 (m110) REVERT: C 378 LYS cc_start: 0.7578 (ttmt) cc_final: 0.7293 (mttm) REVERT: A 36 HIS cc_start: 0.8392 (OUTLIER) cc_final: 0.8184 (t70) REVERT: A 299 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8842 (mm) REVERT: A 357 MET cc_start: 0.7178 (mmm) cc_final: 0.6201 (mpp) REVERT: A 426 ASN cc_start: 0.8298 (t0) cc_final: 0.7978 (t0) REVERT: A 972 PHE cc_start: 0.6409 (OUTLIER) cc_final: 0.5852 (t80) REVERT: B 185 ARG cc_start: 0.6283 (mpp-170) cc_final: 0.6046 (mpp-170) REVERT: B 189 PHE cc_start: 0.6915 (OUTLIER) cc_final: 0.6004 (m-10) outliers start: 81 outliers final: 62 residues processed: 223 average time/residue: 0.2275 time to fit residues: 73.4607 Evaluate side-chains 216 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 150 time to evaluate : 1.304 ------------------------------------------------------------------------------- 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 76 LEU Chi-restraints excluded: chain A residue 161 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 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 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 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 757 THR Chi-restraints excluded: chain A residue 763 ASP 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 58 optimal weight: 0.4980 chunk 120 optimal weight: 0.0980 chunk 97 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 35 optimal weight: 0.2980 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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 841 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11553 Z= 0.165 Angle : 0.557 8.575 15660 Z= 0.296 Chirality : 0.043 0.165 1780 Planarity : 0.004 0.041 2015 Dihedral : 7.534 59.986 1653 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 6.76 % Allowed : 22.93 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.21), residues: 1456 helix: -0.19 (0.23), residues: 514 sheet: -1.53 (0.34), residues: 218 loop : -2.38 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 470 HIS 0.002 0.000 HIS A 319 PHE 0.030 0.001 PHE A 791 TYR 0.012 0.001 TYR C 404 ARG 0.006 0.000 ARG A 692 *********************** 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 243 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 164 time to evaluate : 1.360 Fit side-chains revert: symmetry clash REVERT: C 22 PHE cc_start: 0.6445 (m-80) cc_final: 0.5957 (m-80) REVERT: C 316 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6945 (tt) REVERT: C 322 LYS cc_start: 0.7598 (mmtt) cc_final: 0.6690 (mmtp) REVERT: C 355 ASP cc_start: 0.6798 (t0) cc_final: 0.6350 (t0) REVERT: C 359 GLU cc_start: 0.7839 (tt0) cc_final: 0.7090 (mt-10) REVERT: C 365 GLU cc_start: 0.7574 (mp0) cc_final: 0.7355 (mm-30) REVERT: C 378 LYS cc_start: 0.7618 (ttmt) cc_final: 0.7334 (mttm) REVERT: A 36 HIS cc_start: 0.8368 (OUTLIER) cc_final: 0.8158 (t70) REVERT: A 299 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8814 (mm) REVERT: A 350 SER cc_start: 0.8613 (t) cc_final: 0.8182 (p) REVERT: A 357 MET cc_start: 0.7106 (mmm) cc_final: 0.6560 (mpp) REVERT: A 426 ASN cc_start: 0.8314 (t0) cc_final: 0.7913 (t0) REVERT: A 508 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7766 (mtmt) REVERT: A 972 PHE cc_start: 0.6326 (OUTLIER) cc_final: 0.5835 (t80) REVERT: B 189 PHE cc_start: 0.6857 (OUTLIER) cc_final: 0.5992 (m-10) outliers start: 79 outliers final: 57 residues processed: 228 average time/residue: 0.2451 time to fit residues: 81.7057 Evaluate side-chains 211 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 148 time to evaluate : 1.546 ------------------------------------------------------------------------------- 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 36 HIS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 LEU 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 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 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 27 optimal weight: 0.0670 chunk 82 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 141 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 11 optimal weight: 30.0000 chunk 46 optimal weight: 0.0770 chunk 74 optimal weight: 0.5980 overall best weight: 0.4076 ------------------------------------------------------------------------------- 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 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11553 Z= 0.148 Angle : 0.554 8.075 15660 Z= 0.294 Chirality : 0.043 0.191 1780 Planarity : 0.004 0.039 2015 Dihedral : 7.178 59.644 1650 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 5.22 % Allowed : 24.29 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.21), residues: 1456 helix: 0.13 (0.23), residues: 510 sheet: -1.19 (0.35), residues: 215 loop : -2.20 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 8 HIS 0.002 0.000 HIS B 151 PHE 0.036 0.001 PHE A 791 TYR 0.011 0.001 TYR A 486 ARG 0.008 0.000 ARG A 713 *********************** 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 220 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 159 time to evaluate : 1.337 Fit side-chains REVERT: C 22 PHE cc_start: 0.6323 (m-80) cc_final: 0.5854 (m-80) REVERT: C 322 LYS cc_start: 0.7250 (mmtt) cc_final: 0.6698 (mmtm) REVERT: C 355 ASP cc_start: 0.6795 (t0) cc_final: 0.6384 (t0) REVERT: C 359 GLU cc_start: 0.7762 (tt0) cc_final: 0.7085 (mt-10) REVERT: C 378 LYS cc_start: 0.7531 (ttmt) cc_final: 0.7256 (mttm) REVERT: C 379 ILE cc_start: 0.8209 (mt) cc_final: 0.7997 (mp) REVERT: A 36 HIS cc_start: 0.8361 (OUTLIER) cc_final: 0.8134 (t70) REVERT: A 299 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8793 (mm) REVERT: A 350 SER cc_start: 0.8550 (t) cc_final: 0.8149 (p) REVERT: A 357 MET cc_start: 0.7090 (mmm) cc_final: 0.6515 (mpp) REVERT: A 426 ASN cc_start: 0.8319 (t0) cc_final: 0.7951 (t0) REVERT: A 508 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7789 (mtmt) REVERT: A 972 PHE cc_start: 0.6252 (OUTLIER) cc_final: 0.5782 (t80) REVERT: B 86 LYS cc_start: 0.6454 (mmtt) cc_final: 0.6074 (mmtt) outliers start: 61 outliers final: 47 residues processed: 209 average time/residue: 0.2286 time to fit residues: 69.2789 Evaluate side-chains 193 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 142 time to evaluate : 1.449 ------------------------------------------------------------------------------- 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 372 VAL 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 208 LEU Chi-restraints excluded: chain A residue 212 GLU 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 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 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 641 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 712 LEU 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 887 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 22 VAL Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 63 CYS 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 160 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 overall best weight: 0.8788 ------------------------------------------------------------------------------- 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 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2378 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= 0.195 Angle : 0.571 9.579 15660 Z= 0.302 Chirality : 0.044 0.168 1780 Planarity : 0.004 0.054 2015 Dihedral : 7.039 59.703 1639 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 5.99 % Allowed : 24.64 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.21), residues: 1456 helix: 0.09 (0.23), residues: 518 sheet: -1.19 (0.34), residues: 218 loop : -2.16 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 470 HIS 0.002 0.000 HIS A 265 PHE 0.040 0.001 PHE A 791 TYR 0.013 0.001 TYR A 486 ARG 0.006 0.000 ARG A 692 *********************** 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 215 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 145 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 22 PHE cc_start: 0.6320 (m-80) cc_final: 0.5890 (m-80) REVERT: C 322 LYS cc_start: 0.7220 (mmtt) cc_final: 0.6719 (mmtm) REVERT: C 355 ASP cc_start: 0.6907 (t0) cc_final: 0.6608 (t0) REVERT: C 359 GLU cc_start: 0.7732 (tt0) cc_final: 0.7108 (mt-10) REVERT: C 378 LYS cc_start: 0.7449 (ttmt) cc_final: 0.7186 (mtmm) REVERT: A 36 HIS cc_start: 0.8385 (OUTLIER) cc_final: 0.8138 (t70) REVERT: A 299 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8824 (mm) REVERT: A 357 MET cc_start: 0.7029 (mmm) cc_final: 0.6475 (mpp) REVERT: A 426 ASN cc_start: 0.8314 (t0) cc_final: 0.7953 (t0) REVERT: A 972 PHE cc_start: 0.6312 (OUTLIER) cc_final: 0.5792 (t80) REVERT: B 189 PHE cc_start: 0.6932 (OUTLIER) cc_final: 0.6156 (m-10) outliers start: 70 outliers final: 56 residues processed: 207 average time/residue: 0.2411 time to fit residues: 71.7075 Evaluate side-chains 202 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 142 time to evaluate : 1.323 ------------------------------------------------------------------------------- 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 36 HIS Chi-restraints excluded: chain A residue 42 VAL 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 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 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 641 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 712 LEU 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 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 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 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 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 87 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2385 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= 0.232 Angle : 0.583 7.905 15660 Z= 0.310 Chirality : 0.044 0.176 1780 Planarity : 0.004 0.047 2015 Dihedral : 7.093 59.513 1639 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 5.82 % Allowed : 24.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.22), residues: 1456 helix: 0.12 (0.23), residues: 516 sheet: -1.25 (0.34), residues: 219 loop : -2.15 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.002 0.000 HIS B 151 PHE 0.032 0.001 PHE A 791 TYR 0.015 0.001 TYR A 486 ARG 0.007 0.000 ARG A 692 *********************** 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 217 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 149 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 PHE cc_start: 0.6360 (m-80) cc_final: 0.5943 (m-80) REVERT: C 322 LYS cc_start: 0.7191 (mmtt) cc_final: 0.6626 (mmtp) REVERT: C 347 LYS cc_start: 0.8358 (tmtt) cc_final: 0.7300 (mttt) REVERT: C 355 ASP cc_start: 0.6967 (t0) cc_final: 0.6621 (t0) REVERT: C 359 GLU cc_start: 0.7863 (tt0) cc_final: 0.7222 (mt-10) REVERT: C 378 LYS cc_start: 0.7532 (ttmt) cc_final: 0.7136 (mtmm) REVERT: A 36 HIS cc_start: 0.8391 (OUTLIER) cc_final: 0.8154 (t70) REVERT: A 299 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8841 (mm) REVERT: A 357 MET cc_start: 0.7051 (mmm) cc_final: 0.6115 (mpp) REVERT: A 426 ASN cc_start: 0.8281 (t0) cc_final: 0.7974 (t0) REVERT: A 508 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7566 (mtmt) REVERT: A 972 PHE cc_start: 0.6373 (OUTLIER) cc_final: 0.5843 (t80) REVERT: B 189 PHE cc_start: 0.6935 (OUTLIER) cc_final: 0.6168 (m-10) outliers start: 68 outliers final: 57 residues processed: 206 average time/residue: 0.2445 time to fit residues: 72.1927 Evaluate side-chains 211 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 149 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 36 HIS Chi-restraints excluded: chain A residue 42 VAL 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 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 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 641 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 712 LEU 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 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 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 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 134 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 102 optimal weight: 0.0010 chunk 40 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 overall best weight: 1.2790 ------------------------------------------------------------------------------- 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 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11553 Z= 0.250 Angle : 0.599 7.377 15660 Z= 0.317 Chirality : 0.044 0.153 1780 Planarity : 0.004 0.045 2015 Dihedral : 7.169 59.616 1639 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 5.82 % Allowed : 24.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.21), residues: 1456 helix: 0.09 (0.23), residues: 515 sheet: -1.27 (0.34), residues: 219 loop : -2.15 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.002 0.000 HIS A 265 PHE 0.027 0.001 PHE A 791 TYR 0.016 0.001 TYR A 486 ARG 0.007 0.000 ARG A 692 *********************** 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 220 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 152 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 PHE cc_start: 0.6362 (m-80) cc_final: 0.5952 (m-80) REVERT: C 322 LYS cc_start: 0.7205 (mmtt) cc_final: 0.6689 (mmtp) REVERT: C 347 LYS cc_start: 0.8426 (tmtt) cc_final: 0.7351 (mttt) REVERT: C 355 ASP cc_start: 0.6970 (t0) cc_final: 0.6621 (t0) REVERT: C 359 GLU cc_start: 0.7792 (tt0) cc_final: 0.7208 (mt-10) REVERT: C 376 ARG cc_start: 0.6872 (mmm160) cc_final: 0.6499 (mmm160) REVERT: C 378 LYS cc_start: 0.7519 (ttmt) cc_final: 0.7035 (mtmm) REVERT: A 36 HIS cc_start: 0.8402 (OUTLIER) cc_final: 0.8158 (t70) REVERT: A 299 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8854 (mm) REVERT: A 357 MET cc_start: 0.7096 (mmm) cc_final: 0.6138 (mpp) REVERT: A 508 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7549 (mtmt) REVERT: A 713 ARG cc_start: 0.8170 (ptm-80) cc_final: 0.7885 (ptm-80) REVERT: A 972 PHE cc_start: 0.6393 (OUTLIER) cc_final: 0.5854 (t80) REVERT: B 86 LYS cc_start: 0.6291 (mmtt) cc_final: 0.5990 (mmtt) REVERT: B 189 PHE cc_start: 0.6861 (OUTLIER) cc_final: 0.6078 (m-10) outliers start: 68 outliers final: 60 residues processed: 210 average time/residue: 0.2434 time to fit residues: 73.1867 Evaluate side-chains 211 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 146 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 34 LEU 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 36 HIS Chi-restraints excluded: chain A residue 42 VAL 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 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 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 641 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 712 LEU 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 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 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 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 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 138 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 145 optimal weight: 0.0980 chunk 133 optimal weight: 0.5980 chunk 115 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 0.0980 chunk 92 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11553 Z= 0.157 Angle : 0.570 7.954 15660 Z= 0.304 Chirality : 0.043 0.162 1780 Planarity : 0.004 0.041 2015 Dihedral : 6.977 59.640 1639 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 5.65 % Allowed : 25.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.22), residues: 1456 helix: 0.28 (0.23), residues: 511 sheet: -1.15 (0.35), residues: 216 loop : -2.02 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 8 HIS 0.002 0.000 HIS A 319 PHE 0.023 0.001 PHE A 791 TYR 0.012 0.001 TYR A 486 ARG 0.008 0.000 ARG A 692 ********************** 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 218 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 152 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 22 PHE cc_start: 0.6208 (m-80) cc_final: 0.5820 (m-80) REVERT: C 39 THR cc_start: 0.5844 (m) cc_final: 0.5641 (m) REVERT: C 322 LYS cc_start: 0.7146 (mmtt) cc_final: 0.6645 (mmtm) REVERT: C 347 LYS cc_start: 0.8431 (tmtt) cc_final: 0.7373 (mttt) REVERT: C 355 ASP cc_start: 0.6966 (t0) cc_final: 0.6646 (t0) REVERT: C 359 GLU cc_start: 0.7825 (tt0) cc_final: 0.7410 (mt-10) REVERT: A 36 HIS cc_start: 0.8368 (OUTLIER) cc_final: 0.8133 (t70) REVERT: A 299 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8805 (mm) REVERT: A 350 SER cc_start: 0.8616 (t) cc_final: 0.8193 (p) REVERT: A 357 MET cc_start: 0.7007 (mmm) cc_final: 0.6495 (mpp) REVERT: A 546 LEU cc_start: 0.8069 (mm) cc_final: 0.7522 (mm) REVERT: A 713 ARG cc_start: 0.8072 (ptm-80) cc_final: 0.7131 (ptm-80) REVERT: A 784 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7694 (p90) REVERT: A 972 PHE cc_start: 0.6230 (OUTLIER) cc_final: 0.5798 (t80) REVERT: B 86 LYS cc_start: 0.6317 (mmtt) cc_final: 0.6085 (mmtt) REVERT: B 189 PHE cc_start: 0.6933 (OUTLIER) cc_final: 0.6190 (m-10) outliers start: 66 outliers final: 56 residues processed: 209 average time/residue: 0.2491 time to fit residues: 73.9300 Evaluate side-chains 208 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 147 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 320 THR 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 36 HIS Chi-restraints excluded: chain A residue 42 VAL 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 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 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 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 641 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 712 LEU 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 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 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 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 123 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 14 optimal weight: 0.0770 chunk 21 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- 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 ** A 841 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 = 0.4350 r_free = 0.4350 target = 0.182272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.126513 restraints weight = 16730.581| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.52 r_work: 0.3541 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2683 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= 0.186 Angle : 0.584 8.577 15660 Z= 0.309 Chirality : 0.044 0.332 1780 Planarity : 0.004 0.040 2015 Dihedral : 6.929 59.713 1636 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 5.39 % Allowed : 25.58 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.22), residues: 1456 helix: 0.33 (0.23), residues: 514 sheet: -1.11 (0.35), residues: 216 loop : -1.96 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 470 HIS 0.001 0.000 HIS A 461 PHE 0.024 0.001 PHE A 791 TYR 0.013 0.001 TYR A 486 ARG 0.008 0.000 ARG A 692 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2873.44 seconds wall clock time: 53 minutes 2.92 seconds (3182.92 seconds total)