Starting phenix.real_space_refine on Tue Jun 10 05:01:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hm0_34887/06_2025/8hm0_34887.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hm0_34887/06_2025/8hm0_34887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hm0_34887/06_2025/8hm0_34887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hm0_34887/06_2025/8hm0_34887.map" model { file = "/net/cci-nas-00/data/ceres_data/8hm0_34887/06_2025/8hm0_34887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hm0_34887/06_2025/8hm0_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-5710/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: 7.15, per 1000 atoms: 0.63 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: 2.84 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: 1.39 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: 3.55 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3691 1.34 - 1.46: 2284 1.46 - 1.58: 5489 1.58 - 1.69: 0 1.69 - 1.81: 89 Bond restraints: 11553 Sorted by residual: bond pdb=" C GLU B 20 " pdb=" N PRO B 21 " ideal model delta sigma weight residual 1.336 1.367 -0.031 1.08e-02 8.57e+03 8.26e+00 bond pdb=" CG LEU A 563 " pdb=" CD1 LEU A 563 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.63e+00 bond pdb=" CA ASP A 373 " pdb=" C ASP A 373 " ideal model delta sigma weight residual 1.523 1.508 0.015 1.21e-02 6.83e+03 1.54e+00 bond pdb=" CA SER A 708 " pdb=" C SER A 708 " ideal model delta sigma weight residual 1.532 1.521 0.012 9.60e-03 1.09e+04 1.45e+00 bond pdb=" N VAL B 64 " pdb=" CA VAL B 64 " ideal model delta sigma weight residual 1.474 1.456 0.018 1.57e-02 4.06e+03 1.35e+00 ... (remaining 11548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 15127 1.75 - 3.49: 461 3.49 - 5.24: 56 5.24 - 6.98: 14 6.98 - 8.73: 2 Bond angle restraints: 15660 Sorted by residual: angle pdb=" N THR C 41 " pdb=" CA THR C 41 " pdb=" C THR C 41 " ideal model delta sigma weight residual 114.56 109.83 4.73 1.27e+00 6.20e-01 1.39e+01 angle pdb=" N SER A 780 " pdb=" CA SER A 780 " pdb=" C SER A 780 " ideal model delta sigma weight residual 114.64 109.00 5.64 1.52e+00 4.33e-01 1.38e+01 angle pdb=" C ILE A 609 " pdb=" N SER A 610 " pdb=" CA SER A 610 " ideal model delta sigma weight residual 122.56 117.62 4.94 1.50e+00 4.44e-01 1.08e+01 angle pdb=" C PRO A 721 " pdb=" N PHE A 722 " pdb=" CA PHE A 722 " ideal model delta sigma weight residual 121.54 127.59 -6.05 1.91e+00 2.74e-01 1.00e+01 angle pdb=" N THR A 752 " pdb=" CA THR A 752 " pdb=" C THR A 752 " ideal model delta sigma weight residual 114.62 111.03 3.59 1.14e+00 7.69e-01 9.92e+00 ... (remaining 15655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6049 17.88 - 35.77: 701 35.77 - 53.65: 179 53.65 - 71.54: 39 71.54 - 89.42: 17 Dihedral angle restraints: 6985 sinusoidal: 2624 harmonic: 4361 Sorted by residual: dihedral pdb=" CA GLY A 434 " pdb=" C GLY A 434 " pdb=" N LYS A 435 " pdb=" CA LYS A 435 " ideal model delta harmonic sigma weight residual 180.00 151.72 28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA GLU C 365 " pdb=" C GLU C 365 " pdb=" N ALA C 366 " pdb=" CA ALA C 366 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA SER B 153 " pdb=" C SER B 153 " pdb=" N VAL B 154 " pdb=" CA VAL B 154 " ideal model delta harmonic sigma weight residual 180.00 154.12 25.88 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 6982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 972 0.031 - 0.062: 544 0.062 - 0.093: 177 0.093 - 0.125: 72 0.125 - 0.156: 15 Chirality restraints: 1780 Sorted by residual: chirality pdb=" CA ASP A 400 " pdb=" N ASP A 400 " pdb=" C ASP A 400 " pdb=" CB ASP A 400 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CB ILE A 739 " pdb=" CA ILE A 739 " pdb=" CG1 ILE A 739 " pdb=" CG2 ILE A 739 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CB VAL B 178 " pdb=" CA VAL B 178 " pdb=" CG1 VAL B 178 " pdb=" CG2 VAL B 178 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.55e-01 ... (remaining 1777 not shown) Planarity restraints: 2015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 554 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO A 555 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 555 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 555 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 593 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO A 594 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 594 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 594 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 564 " -0.028 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO A 565 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 565 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 565 " -0.023 5.00e-02 4.00e+02 ... (remaining 2012 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 558 2.71 - 3.26: 11439 3.26 - 3.80: 17513 3.80 - 4.35: 22258 4.35 - 4.90: 37335 Nonbonded interactions: 89103 Sorted by model distance: nonbonded pdb=" N ASP A 439 " pdb=" OD1 ASP A 439 " model vdw 2.162 3.120 nonbonded pdb=" O ALA C 5 " pdb=" OG1 THR C 8 " model vdw 2.213 3.040 nonbonded pdb=" O LYS A 973 " pdb=" OG SER A 977 " model vdw 2.220 3.040 nonbonded pdb=" NH1 ARG A 23 " pdb=" OG1 THR A 29 " model vdw 2.224 3.120 nonbonded pdb=" OE2 GLU A 205 " pdb=" NH1 ARG A 223 " model vdw 2.244 3.120 ... (remaining 89098 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.430 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 28.770 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11553 Z= 0.220 Angle : 0.724 8.729 15660 Z= 0.433 Chirality : 0.044 0.156 1780 Planarity : 0.004 0.045 2015 Dihedral : 17.210 89.420 4157 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.82 % Favored : 90.11 % Rotamer: Outliers : 9.92 % Allowed : 20.62 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.16319 ( 412) hydrogen bonds : angle 7.27628 ( 1185) covalent geometry : bond 0.00481 (11553) covalent geometry : angle 0.72416 (15660) *********************** 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 : 1.491 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: 0.2452 time to fit residues: 93.1613 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 : 1.241 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.179105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.127437 restraints weight = 16715.584| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.89 r_work: 0.3512 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 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= 0.125 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 Details of bonding type rmsd hydrogen bonds : bond 0.04201 ( 412) hydrogen bonds : angle 5.27078 ( 1185) covalent geometry : bond 0.00260 (11553) covalent geometry : angle 0.59556 (15660) *********************** 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 : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 355 ASP cc_start: 0.7093 (t0) cc_final: 0.6542 (t0) REVERT: C 359 GLU cc_start: 0.8001 (tt0) cc_final: 0.7165 (mt-10) REVERT: C 365 GLU cc_start: 0.7581 (mp0) cc_final: 0.7037 (mp0) REVERT: C 374 ASN cc_start: 0.7168 (m-40) cc_final: 0.6824 (m110) REVERT: C 376 ARG cc_start: 0.6830 (mmm160) cc_final: 0.6505 (mmm160) REVERT: A 36 HIS cc_start: 0.8647 (OUTLIER) cc_final: 0.8415 (t70) REVERT: A 129 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7663 (pm20) REVERT: A 299 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.8970 (mm) REVERT: A 350 SER cc_start: 0.8797 (t) cc_final: 0.8249 (p) REVERT: A 357 MET cc_start: 0.7204 (mmm) cc_final: 0.6552 (mpp) REVERT: A 508 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7913 (mtmt) REVERT: A 576 ASN cc_start: 0.7871 (m110) cc_final: 0.7539 (m110) REVERT: A 712 LEU cc_start: 0.5818 (pt) cc_final: 0.5557 (tp) REVERT: B 65 CYS cc_start: 0.8275 (m) cc_final: 0.7908 (m) outliers start: 79 outliers final: 50 residues processed: 229 average time/residue: 0.2370 time to fit residues: 76.9521 Evaluate side-chains 199 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 146 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 127 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 31 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 145 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 102 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.181933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.126476 restraints weight = 17181.699| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.54 r_work: 0.3581 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11553 Z= 0.117 Angle : 0.558 6.797 15660 Z= 0.299 Chirality : 0.043 0.200 1780 Planarity : 0.004 0.059 2015 Dihedral : 8.163 58.898 1664 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 6.93 % Allowed : 22.41 % Favored : 70.66 % 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: -2.61 (0.21), residues: 1456 helix: -0.59 (0.22), residues: 513 sheet: -1.88 (0.32), residues: 231 loop : -2.59 (0.22), residues: 712 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 0.035 0.001 PHE C 410 TYR 0.011 0.001 TYR A 486 ARG 0.015 0.000 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 412) hydrogen bonds : angle 4.97015 ( 1185) covalent geometry : bond 0.00258 (11553) covalent geometry : angle 0.55785 (15660) *********************** 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 239 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 158 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 355 ASP cc_start: 0.7263 (t0) cc_final: 0.6821 (t0) REVERT: C 359 GLU cc_start: 0.8231 (tt0) cc_final: 0.7401 (mt-10) REVERT: C 365 GLU cc_start: 0.7776 (mp0) cc_final: 0.7488 (mm-30) REVERT: C 374 ASN cc_start: 0.7223 (m-40) cc_final: 0.6859 (m110) REVERT: C 376 ARG cc_start: 0.6842 (mmm160) cc_final: 0.6462 (mmm160) REVERT: A 129 GLU cc_start: 0.8375 (tm-30) cc_final: 0.7727 (pm20) REVERT: A 299 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.9019 (mm) REVERT: A 350 SER cc_start: 0.8850 (t) cc_final: 0.8307 (p) REVERT: A 357 MET cc_start: 0.7223 (mmm) cc_final: 0.6611 (mpp) REVERT: A 426 ASN cc_start: 0.8476 (t0) cc_final: 0.8203 (t0) REVERT: A 508 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7887 (mtmt) REVERT: B 52 GLN cc_start: 0.8726 (tp40) cc_final: 0.8505 (tp40) REVERT: B 185 ARG cc_start: 0.6556 (mpp-170) cc_final: 0.6232 (mpp-170) outliers start: 81 outliers final: 53 residues processed: 223 average time/residue: 0.2278 time to fit residues: 73.3533 Evaluate side-chains 204 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 149 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 GLU 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 42 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 78 ILE 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 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 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 578 LEU 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 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 830 GLU Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 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 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 Chi-restraints excluded: chain B residue 165 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 116 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 103 optimal weight: 0.0870 chunk 29 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 overall best weight: 1.7762 ------------------------------------------------------------------------------- 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 779 ASN A 860 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.178098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.121446 restraints weight = 16971.418| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.51 r_work: 0.3525 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11553 Z= 0.213 Angle : 0.626 7.398 15660 Z= 0.331 Chirality : 0.045 0.157 1780 Planarity : 0.004 0.036 2015 Dihedral : 8.026 59.866 1652 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 6.67 % Allowed : 23.35 % 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: -2.57 (0.21), residues: 1456 helix: -0.64 (0.22), residues: 524 sheet: -1.75 (0.33), residues: 218 loop : -2.54 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 470 HIS 0.007 0.001 HIS A 36 PHE 0.027 0.002 PHE C 410 TYR 0.019 0.002 TYR A 486 ARG 0.006 0.000 ARG A 713 Details of bonding type rmsd hydrogen bonds : bond 0.04433 ( 412) hydrogen bonds : angle 5.05235 ( 1185) covalent geometry : bond 0.00505 (11553) covalent geometry : angle 0.62592 (15660) *********************** 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 226 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 148 time to evaluate : 1.204 Fit side-chains revert: symmetry clash REVERT: C 355 ASP cc_start: 0.7404 (t0) cc_final: 0.7148 (t0) REVERT: C 359 GLU cc_start: 0.8271 (tt0) cc_final: 0.7612 (mt-10) REVERT: C 365 GLU cc_start: 0.7758 (mp0) cc_final: 0.7487 (mm-30) REVERT: C 374 ASN cc_start: 0.7222 (m-40) cc_final: 0.6839 (m110) REVERT: C 378 LYS cc_start: 0.7775 (ttmt) cc_final: 0.7318 (mttm) REVERT: A 129 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7663 (pm20) REVERT: A 299 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9115 (mm) REVERT: A 357 MET cc_start: 0.7299 (mmm) cc_final: 0.6302 (mpp) REVERT: A 779 ASN cc_start: 0.8320 (OUTLIER) cc_final: 0.8019 (p0) REVERT: A 972 PHE cc_start: 0.6092 (OUTLIER) cc_final: 0.5553 (t80) REVERT: B 185 ARG cc_start: 0.6465 (mpp-170) cc_final: 0.6192 (mpp-170) REVERT: B 189 PHE cc_start: 0.6697 (OUTLIER) cc_final: 0.5805 (m-10) outliers start: 78 outliers final: 62 residues processed: 213 average time/residue: 0.2428 time to fit residues: 75.3129 Evaluate side-chains 202 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 136 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 GLU 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 42 VAL Chi-restraints excluded: chain A residue 76 LEU 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 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 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 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 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 778 ILE Chi-restraints excluded: chain A residue 779 ASN 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 153 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 139 optimal weight: 0.5980 chunk 4 optimal weight: 0.0040 chunk 54 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.181476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.125769 restraints weight = 16878.790| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.53 r_work: 0.3508 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2010 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= 0.115 Angle : 0.560 8.317 15660 Z= 0.298 Chirality : 0.043 0.166 1780 Planarity : 0.004 0.038 2015 Dihedral : 7.443 59.588 1648 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 5.99 % Allowed : 23.52 % 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: -2.14 (0.21), residues: 1456 helix: -0.23 (0.23), residues: 519 sheet: -1.42 (0.34), residues: 208 loop : -2.35 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 8 HIS 0.002 0.000 HIS A 36 PHE 0.030 0.001 PHE A 791 TYR 0.012 0.001 TYR A 486 ARG 0.006 0.000 ARG A 692 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 412) hydrogen bonds : angle 4.79339 ( 1185) covalent geometry : bond 0.00256 (11553) covalent geometry : angle 0.56027 (15660) *********************** 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 226 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 156 time to evaluate : 1.454 Fit side-chains revert: symmetry clash REVERT: C 22 PHE cc_start: 0.6168 (m-80) cc_final: 0.5749 (m-80) REVERT: C 322 LYS cc_start: 0.7506 (mmtt) cc_final: 0.6587 (mmtm) REVERT: C 355 ASP cc_start: 0.7335 (t0) cc_final: 0.6882 (t0) REVERT: C 359 GLU cc_start: 0.8168 (tt0) cc_final: 0.7319 (mt-10) REVERT: C 365 GLU cc_start: 0.7709 (mp0) cc_final: 0.7426 (mm-30) REVERT: C 374 ASN cc_start: 0.7187 (m-40) cc_final: 0.6831 (m110) REVERT: C 378 LYS cc_start: 0.7844 (ttmt) cc_final: 0.7394 (mttm) REVERT: A 129 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7474 (pm20) REVERT: A 143 ASP cc_start: 0.7116 (p0) cc_final: 0.6665 (p0) REVERT: A 299 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.9049 (mm) REVERT: A 357 MET cc_start: 0.7196 (mmm) cc_final: 0.6573 (mpp) REVERT: A 426 ASN cc_start: 0.8417 (t0) cc_final: 0.8165 (t0) REVERT: A 791 PHE cc_start: 0.7326 (t80) cc_final: 0.7118 (t80) REVERT: A 972 PHE cc_start: 0.5970 (OUTLIER) cc_final: 0.5587 (t80) REVERT: B 185 ARG cc_start: 0.6241 (mpp-170) cc_final: 0.6037 (mpp-170) outliers start: 70 outliers final: 53 residues processed: 215 average time/residue: 0.2318 time to fit residues: 72.3585 Evaluate side-chains 204 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 149 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 LEU 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 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 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 696 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 778 ILE 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 54 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 19 optimal weight: 20.0000 chunk 97 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 98 optimal weight: 0.0980 chunk 10 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** B 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.180113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.124107 restraints weight = 17119.772| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.55 r_work: 0.3481 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11553 Z= 0.151 Angle : 0.577 7.999 15660 Z= 0.306 Chirality : 0.044 0.179 1780 Planarity : 0.004 0.047 2015 Dihedral : 7.279 59.432 1641 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 6.24 % Allowed : 23.52 % Favored : 70.23 % 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: -2.01 (0.21), residues: 1456 helix: -0.09 (0.23), residues: 511 sheet: -1.52 (0.34), residues: 218 loop : -2.23 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.005 0.001 HIS A 36 PHE 0.021 0.001 PHE C 410 TYR 0.015 0.001 TYR A 486 ARG 0.006 0.000 ARG A 692 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 412) hydrogen bonds : angle 4.76605 ( 1185) covalent geometry : bond 0.00352 (11553) covalent geometry : angle 0.57701 (15660) *********************** 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 224 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 151 time to evaluate : 1.201 Fit side-chains revert: symmetry clash REVERT: C 22 PHE cc_start: 0.6194 (m-80) cc_final: 0.5800 (m-80) REVERT: C 322 LYS cc_start: 0.7125 (mmtt) cc_final: 0.6476 (mmtm) REVERT: C 355 ASP cc_start: 0.7381 (t0) cc_final: 0.6926 (t0) REVERT: C 359 GLU cc_start: 0.8230 (tt0) cc_final: 0.7408 (mt-10) REVERT: C 365 GLU cc_start: 0.7722 (mp0) cc_final: 0.7430 (mm-30) REVERT: C 374 ASN cc_start: 0.7281 (m-40) cc_final: 0.7058 (m110) REVERT: C 378 LYS cc_start: 0.7743 (ttmt) cc_final: 0.7274 (mttm) REVERT: C 379 ILE cc_start: 0.8309 (mt) cc_final: 0.8049 (mp) REVERT: A 129 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7502 (pm20) REVERT: A 143 ASP cc_start: 0.7093 (p0) cc_final: 0.6878 (p0) REVERT: A 299 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.9076 (mm) REVERT: A 357 MET cc_start: 0.7213 (mmm) cc_final: 0.6577 (mpp) REVERT: A 426 ASN cc_start: 0.8426 (t0) cc_final: 0.8147 (t0) REVERT: A 508 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7992 (mtmt) REVERT: A 972 PHE cc_start: 0.6009 (OUTLIER) cc_final: 0.5585 (t80) REVERT: B 189 PHE cc_start: 0.6945 (OUTLIER) cc_final: 0.6104 (m-10) outliers start: 73 outliers final: 57 residues processed: 213 average time/residue: 0.2605 time to fit residues: 79.8939 Evaluate side-chains 204 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 143 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 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 403 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 696 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 757 THR Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 784 PHE Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 189 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 12 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 55 optimal weight: 0.0070 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 overall best weight: 1.0004 ------------------------------------------------------------------------------- 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 576 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 = 0.4330 r_free = 0.4330 target = 0.180473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.124471 restraints weight = 17142.088| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.55 r_work: 0.3555 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2202 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= 0.143 Angle : 0.580 9.559 15660 Z= 0.308 Chirality : 0.044 0.167 1780 Planarity : 0.004 0.040 2015 Dihedral : 7.223 59.612 1638 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 6.24 % Allowed : 23.61 % Favored : 70.15 % 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: -1.91 (0.21), residues: 1456 helix: -0.03 (0.23), residues: 517 sheet: -1.27 (0.35), residues: 208 loop : -2.24 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.004 0.001 HIS A 36 PHE 0.037 0.001 PHE A 791 TYR 0.015 0.001 TYR A 486 ARG 0.007 0.000 ARG A 692 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 412) hydrogen bonds : angle 4.72893 ( 1185) covalent geometry : bond 0.00333 (11553) covalent geometry : angle 0.57985 (15660) *********************** 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 224 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 151 time to evaluate : 1.492 Fit side-chains revert: symmetry clash REVERT: C 22 PHE cc_start: 0.6095 (m-80) cc_final: 0.5707 (m-80) REVERT: C 322 LYS cc_start: 0.6997 (mmtt) cc_final: 0.6488 (mmtm) REVERT: C 355 ASP cc_start: 0.7357 (t0) cc_final: 0.6998 (t0) REVERT: C 359 GLU cc_start: 0.8188 (tt0) cc_final: 0.7442 (mt-10) REVERT: C 365 GLU cc_start: 0.7711 (mp0) cc_final: 0.7433 (mm-30) REVERT: C 378 LYS cc_start: 0.7707 (ttmt) cc_final: 0.7262 (mtmm) REVERT: A 129 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7483 (pm20) REVERT: A 143 ASP cc_start: 0.7050 (p0) cc_final: 0.6825 (p0) REVERT: A 299 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.9066 (mm) REVERT: A 357 MET cc_start: 0.7217 (mmm) cc_final: 0.6233 (mpp) REVERT: A 426 ASN cc_start: 0.8417 (t0) cc_final: 0.7980 (t0) REVERT: A 508 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7918 (mtmt) REVERT: A 711 MET cc_start: 0.2733 (tmm) cc_final: 0.2475 (tmm) REVERT: A 972 PHE cc_start: 0.6027 (OUTLIER) cc_final: 0.5611 (t80) REVERT: B 189 PHE cc_start: 0.6938 (OUTLIER) cc_final: 0.6098 (m-10) outliers start: 73 outliers final: 58 residues processed: 213 average time/residue: 0.2744 time to fit residues: 83.9577 Evaluate side-chains 208 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 146 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 GLU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 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 696 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 757 THR Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 784 PHE Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 SER 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 83 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 81 optimal weight: 0.0470 chunk 87 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.178471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.126006 restraints weight = 16859.853| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.88 r_work: 0.3488 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11553 Z= 0.120 Angle : 0.565 7.667 15660 Z= 0.301 Chirality : 0.043 0.187 1780 Planarity : 0.004 0.044 2015 Dihedral : 7.109 59.058 1638 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 5.56 % Allowed : 24.38 % Favored : 70.06 % 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: -1.72 (0.22), residues: 1456 helix: 0.09 (0.23), residues: 521 sheet: -1.17 (0.35), residues: 209 loop : -2.10 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 8 HIS 0.003 0.000 HIS A 36 PHE 0.036 0.001 PHE A 791 TYR 0.012 0.001 TYR A 486 ARG 0.007 0.000 ARG A 692 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 412) hydrogen bonds : angle 4.64407 ( 1185) covalent geometry : bond 0.00270 (11553) covalent geometry : angle 0.56512 (15660) *********************** 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: 65 poor density : 152 time to evaluate : 1.180 Fit side-chains REVERT: C 22 PHE cc_start: 0.6113 (m-80) cc_final: 0.5758 (m-80) REVERT: C 322 LYS cc_start: 0.6817 (mmtt) cc_final: 0.6207 (mmtp) REVERT: C 347 LYS cc_start: 0.8399 (tmtt) cc_final: 0.7250 (mttt) REVERT: C 355 ASP cc_start: 0.7243 (t0) cc_final: 0.6830 (t0) REVERT: C 359 GLU cc_start: 0.8158 (tt0) cc_final: 0.7396 (mt-10) REVERT: C 365 GLU cc_start: 0.7725 (mp0) cc_final: 0.7447 (mm-30) REVERT: C 376 ARG cc_start: 0.6830 (mmm160) cc_final: 0.6602 (tpp-160) REVERT: A 129 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7458 (pm20) REVERT: A 143 ASP cc_start: 0.6848 (p0) cc_final: 0.6522 (p0) REVERT: A 299 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.8998 (mm) REVERT: A 350 SER cc_start: 0.8797 (t) cc_final: 0.8219 (p) REVERT: A 357 MET cc_start: 0.7074 (mmm) cc_final: 0.6459 (mpp) REVERT: A 426 ASN cc_start: 0.8362 (t0) cc_final: 0.7925 (t0) REVERT: A 508 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7836 (mtmt) REVERT: A 711 MET cc_start: 0.2386 (tmm) cc_final: 0.2154 (tmm) REVERT: A 779 ASN cc_start: 0.7803 (p0) cc_final: 0.7596 (p0) REVERT: A 972 PHE cc_start: 0.5947 (OUTLIER) cc_final: 0.5582 (t80) REVERT: B 86 LYS cc_start: 0.6313 (mmtt) cc_final: 0.5956 (mmtt) REVERT: B 189 PHE cc_start: 0.6888 (OUTLIER) cc_final: 0.6095 (m-10) outliers start: 65 outliers final: 51 residues processed: 208 average time/residue: 0.2852 time to fit residues: 89.5426 Evaluate side-chains 199 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 144 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 GLU 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 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 280 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 696 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 757 THR Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 784 PHE Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 839 HIS Chi-restraints excluded: chain A residue 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 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 19 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.181400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.125462 restraints weight = 17053.586| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.54 r_work: 0.3572 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11553 Z= 0.129 Angle : 0.573 8.915 15660 Z= 0.303 Chirality : 0.043 0.169 1780 Planarity : 0.004 0.058 2015 Dihedral : 6.985 59.299 1635 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 5.30 % Allowed : 24.72 % 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: -1.61 (0.22), residues: 1456 helix: 0.19 (0.23), residues: 517 sheet: -1.10 (0.35), residues: 215 loop : -2.03 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 470 HIS 0.004 0.000 HIS A 36 PHE 0.029 0.001 PHE C 407 TYR 0.013 0.001 TYR A 486 ARG 0.007 0.000 ARG A 692 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 412) hydrogen bonds : angle 4.63543 ( 1185) covalent geometry : bond 0.00297 (11553) covalent geometry : angle 0.57270 (15660) *********************** 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 213 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 151 time to evaluate : 1.204 Fit side-chains REVERT: C 22 PHE cc_start: 0.6110 (m-80) cc_final: 0.5731 (m-80) REVERT: C 322 LYS cc_start: 0.7019 (mmtt) cc_final: 0.6510 (mmtp) REVERT: C 347 LYS cc_start: 0.8414 (tmtt) cc_final: 0.7253 (mttt) REVERT: C 355 ASP cc_start: 0.7414 (t0) cc_final: 0.7017 (t0) REVERT: C 359 GLU cc_start: 0.8132 (tt0) cc_final: 0.7529 (mt-10) REVERT: C 365 GLU cc_start: 0.7869 (mp0) cc_final: 0.7589 (mm-30) REVERT: C 376 ARG cc_start: 0.6941 (mmm160) cc_final: 0.6491 (mmm160) REVERT: C 378 LYS cc_start: 0.7795 (ttmt) cc_final: 0.7146 (mttm) REVERT: A 129 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7512 (pm20) REVERT: A 143 ASP cc_start: 0.7022 (p0) cc_final: 0.6582 (p0) REVERT: A 299 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.9056 (mm) REVERT: A 350 SER cc_start: 0.8886 (t) cc_final: 0.8312 (p) REVERT: A 357 MET cc_start: 0.7106 (mmm) cc_final: 0.6522 (mpp) REVERT: A 426 ASN cc_start: 0.8409 (t0) cc_final: 0.7983 (t0) REVERT: A 508 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7815 (mtmt) REVERT: A 711 MET cc_start: 0.2369 (tmm) cc_final: 0.2124 (tmm) REVERT: A 784 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7904 (p90) REVERT: A 972 PHE cc_start: 0.6006 (OUTLIER) cc_final: 0.5605 (t80) REVERT: B 189 PHE cc_start: 0.6817 (OUTLIER) cc_final: 0.6019 (m-10) outliers start: 62 outliers final: 53 residues processed: 201 average time/residue: 0.2217 time to fit residues: 64.3183 Evaluate side-chains 204 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 146 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 GLU 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 C residue 419 ASP Chi-restraints excluded: chain A residue 10 GLU 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 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 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 696 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 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 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 36 optimal weight: 0.3980 chunk 92 optimal weight: 0.5980 chunk 139 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 62 optimal weight: 0.0010 chunk 41 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 0.0020 chunk 47 optimal weight: 0.0570 chunk 73 optimal weight: 0.9990 overall best weight: 0.2112 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.184112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.131295 restraints weight = 16692.097| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.45 r_work: 0.3587 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11553 Z= 0.103 Angle : 0.558 8.655 15660 Z= 0.296 Chirality : 0.043 0.172 1780 Planarity : 0.004 0.049 2015 Dihedral : 6.674 59.451 1635 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.28 % Allowed : 26.01 % Favored : 69.72 % 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: -1.39 (0.22), residues: 1456 helix: 0.45 (0.24), residues: 510 sheet: -0.99 (0.35), residues: 216 loop : -1.94 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 8 HIS 0.002 0.000 HIS A 319 PHE 0.038 0.001 PHE C 407 TYR 0.011 0.001 TYR A 486 ARG 0.008 0.000 ARG A 692 Details of bonding type rmsd hydrogen bonds : bond 0.03169 ( 412) hydrogen bonds : angle 4.50500 ( 1185) covalent geometry : bond 0.00220 (11553) covalent geometry : angle 0.55847 (15660) ********************** 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 205 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 155 time to evaluate : 1.199 Fit side-chains REVERT: C 22 PHE cc_start: 0.5908 (m-80) cc_final: 0.5562 (m-80) REVERT: C 322 LYS cc_start: 0.7074 (mmtt) cc_final: 0.6399 (mmtm) REVERT: C 347 LYS cc_start: 0.8406 (tmtt) cc_final: 0.7214 (mttt) REVERT: C 355 ASP cc_start: 0.7428 (t0) cc_final: 0.7058 (t0) REVERT: C 359 GLU cc_start: 0.8099 (tt0) cc_final: 0.7644 (mt-10) REVERT: C 365 GLU cc_start: 0.7809 (mp0) cc_final: 0.7571 (mm-30) REVERT: C 376 ARG cc_start: 0.6978 (mmm160) cc_final: 0.6586 (mmm160) REVERT: C 378 LYS cc_start: 0.7805 (ttmt) cc_final: 0.7531 (tppt) REVERT: A 129 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7422 (pm20) REVERT: A 143 ASP cc_start: 0.6816 (p0) cc_final: 0.6404 (p0) REVERT: A 299 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.8999 (mm) REVERT: A 350 SER cc_start: 0.8767 (t) cc_final: 0.8181 (p) REVERT: A 357 MET cc_start: 0.7089 (mmm) cc_final: 0.6441 (mpp) REVERT: A 426 ASN cc_start: 0.8421 (t0) cc_final: 0.8023 (t0) REVERT: A 972 PHE cc_start: 0.5916 (OUTLIER) cc_final: 0.5572 (t80) REVERT: B 86 LYS cc_start: 0.6412 (mmtt) cc_final: 0.6124 (mmtt) outliers start: 50 outliers final: 39 residues processed: 196 average time/residue: 0.2195 time to fit residues: 62.2074 Evaluate side-chains 188 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 GLU 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 C residue 419 ASP 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 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 371 ILE 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 533 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 748 VAL Chi-restraints excluded: chain A residue 749 TYR Chi-restraints excluded: chain A residue 757 THR 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 972 PHE 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 116 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 160 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 75 optimal weight: 0.0470 chunk 32 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 90 optimal weight: 0.0040 chunk 98 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 111 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.4492 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.184048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.128451 restraints weight = 16963.746| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.58 r_work: 0.3561 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11553 Z= 0.110 Angle : 0.573 8.273 15660 Z= 0.299 Chirality : 0.044 0.348 1780 Planarity : 0.004 0.048 2015 Dihedral : 6.563 59.130 1629 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 4.02 % Allowed : 26.35 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.31 (0.22), residues: 1456 helix: 0.49 (0.23), residues: 516 sheet: -0.96 (0.35), residues: 217 loop : -1.89 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 8 HIS 0.003 0.000 HIS A 36 PHE 0.038 0.001 PHE C 407 TYR 0.011 0.001 TYR A 486 ARG 0.008 0.000 ARG A 692 Details of bonding type rmsd hydrogen bonds : bond 0.03306 ( 412) hydrogen bonds : angle 4.46384 ( 1185) covalent geometry : bond 0.00247 (11553) covalent geometry : angle 0.57284 (15660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9262.71 seconds wall clock time: 164 minutes 19.09 seconds (9859.09 seconds total)