Starting phenix.real_space_refine on Sun Apr 27 20:59:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n49_48871/04_2025/9n49_48871.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n49_48871/04_2025/9n49_48871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n49_48871/04_2025/9n49_48871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n49_48871/04_2025/9n49_48871.map" model { file = "/net/cci-nas-00/data/ceres_data/9n49_48871/04_2025/9n49_48871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n49_48871/04_2025/9n49_48871.cif" } resolution = 3.0 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= -0.001 sd= 0.017 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 19 5.16 5 C 4081 2.51 5 N 1176 2.21 5 O 1233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6509 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 229 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 1, 'TRANS': 44} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 106 Chain: "G" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 1921 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 171} Link IDs: {'PTRANS': 6, 'TRANS': 312} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 583 Unresolved non-hydrogen angles: 735 Unresolved non-hydrogen dihedrals: 451 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 12, 'TYR:plan': 1, 'ASN:plan1': 9, 'HIS:plan': 1, 'PHE:plan': 6, 'GLU:plan': 21, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 319 Chain: "M" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2317 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 268} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "N" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 658 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 82} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "P" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 632 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 752 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 96} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 14.24, per 1000 atoms: 2.19 Number of scatterers: 6509 At special positions: 0 Unit cell: (111.52, 85.68, 167.28, 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 19 16.00 O 1233 8.00 N 1176 7.00 C 4081 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: 1.71 Conformation dependent library (CDL) restraints added in 1.1 seconds 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1738 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 6 sheets defined 51.9% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'F' and resid 514 through 543 removed outlier: 3.602A pdb=" N GLU F 530 " --> pdb=" O ARG F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 559 removed outlier: 3.943A pdb=" N VAL F 547 " --> pdb=" O ASP F 543 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA F 548 " --> pdb=" O PRO F 544 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 18 removed outlier: 3.532A pdb=" N GLY G 18 " --> pdb=" O LEU G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 28 Processing helix chain 'G' and resid 30 through 44 removed outlier: 3.613A pdb=" N ALA G 42 " --> pdb=" O SER G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 63 removed outlier: 3.657A pdb=" N GLU G 62 " --> pdb=" O GLU G 58 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA G 63 " --> pdb=" O PHE G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 72 removed outlier: 4.493A pdb=" N ALA G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU G 69 " --> pdb=" O GLN G 65 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN G 72 " --> pdb=" O ALA G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 85 removed outlier: 3.700A pdb=" N LEU G 85 " --> pdb=" O LEU G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 101 removed outlier: 3.935A pdb=" N ARG G 101 " --> pdb=" O ILE G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 110 Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'G' and resid 114 through 123 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 138 through 149 Processing helix chain 'G' and resid 150 through 163 Processing helix chain 'G' and resid 168 through 184 Processing helix chain 'G' and resid 196 through 205 removed outlier: 3.650A pdb=" N LEU G 205 " --> pdb=" O GLU G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 222 Processing helix chain 'G' and resid 222 through 234 removed outlier: 3.568A pdb=" N PHE G 234 " --> pdb=" O ILE G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 242 removed outlier: 4.224A pdb=" N VAL G 240 " --> pdb=" O GLU G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 252 removed outlier: 3.690A pdb=" N GLN G 252 " --> pdb=" O GLN G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 265 removed outlier: 4.402A pdb=" N GLY G 265 " --> pdb=" O ILE G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 275 Processing helix chain 'G' and resid 279 through 293 Processing helix chain 'G' and resid 297 through 319 removed outlier: 3.797A pdb=" N VAL G 301 " --> pdb=" O ARG G 297 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 74 removed outlier: 3.999A pdb=" N GLU M 59 " --> pdb=" O GLU M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 96 Processing helix chain 'M' and resid 119 through 131 Processing helix chain 'M' and resid 147 through 171 removed outlier: 3.601A pdb=" N LEU M 160 " --> pdb=" O ARG M 156 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA M 171 " --> pdb=" O ASP M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 225 Processing helix chain 'M' and resid 227 through 233 removed outlier: 3.927A pdb=" N ASN M 233 " --> pdb=" O GLU M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 239 through 256 removed outlier: 4.148A pdb=" N HIS M 256 " --> pdb=" O ARG M 252 " (cutoff:3.500A) Processing helix chain 'M' and resid 272 through 278 Processing helix chain 'N' and resid 75 through 80 Processing helix chain 'N' and resid 127 through 137 Processing helix chain 'P' and resid 74 through 81 Processing helix chain 'P' and resid 128 through 134 removed outlier: 3.962A pdb=" N MET P 132 " --> pdb=" O PRO P 128 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG P 133 " --> pdb=" O SER P 129 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 81 removed outlier: 3.894A pdb=" N ARG Q 80 " --> pdb=" O LYS Q 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 127 through 136 Processing sheet with id=AA1, first strand: chain 'M' and resid 35 through 37 removed outlier: 7.082A pdb=" N ILE P 99 " --> pdb=" O ILE P 106 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLN P 108 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU P 97 " --> pdb=" O GLN P 108 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP P 98 " --> pdb=" O GLU P 67 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N THR Q 74 " --> pdb=" O PRO P 61 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LYS P 63 " --> pdb=" O ARG Q 72 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ARG Q 72 " --> pdb=" O LYS P 63 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR P 65 " --> pdb=" O ARG Q 70 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ARG Q 70 " --> pdb=" O THR P 65 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N GLU P 67 " --> pdb=" O LEU Q 68 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU Q 68 " --> pdb=" O GLU P 67 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP Q 98 " --> pdb=" O GLU Q 67 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA Q 107 " --> pdb=" O ILE Q 99 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE Q 101 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU Q 105 " --> pdb=" O ILE Q 101 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ILE Q 106 " --> pdb=" O ILE Q 125 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE Q 125 " --> pdb=" O ILE Q 106 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLN Q 108 " --> pdb=" O THR Q 123 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N TYR Q 118 " --> pdb=" O LEU P 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 35 through 37 removed outlier: 6.695A pdb=" N GLU P 110 " --> pdb=" O ILE P 122 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ILE P 122 " --> pdb=" O GLU P 110 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL P 112 " --> pdb=" O VAL P 120 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL P 120 " --> pdb=" O VAL P 112 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL P 114 " --> pdb=" O TYR P 118 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N TYR P 118 " --> pdb=" O VAL P 114 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR P 118 " --> pdb=" O LEU Q 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 78 through 81 Processing sheet with id=AA4, first strand: chain 'M' and resid 78 through 81 removed outlier: 6.639A pdb=" N LEU M 102 " --> pdb=" O SER M 182 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N SER M 182 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU M 104 " --> pdb=" O VAL M 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 258 through 260 Processing sheet with id=AA6, first strand: chain 'M' and resid 283 through 286 removed outlier: 3.933A pdb=" N TYR N 118 " --> pdb=" O ILE M 286 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLN N 108 " --> pdb=" O THR N 123 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE N 99 " --> pdb=" O ILE N 106 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLN N 108 " --> pdb=" O LEU N 97 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU N 97 " --> pdb=" O GLN N 108 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASP N 98 " --> pdb=" O GLU N 67 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU N 67 " --> pdb=" O ASP N 98 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA M 266 " --> pdb=" O VAL N 66 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE M 293 " --> pdb=" O ASN M 264 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE M 292 " --> pdb=" O THR M 303 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THR M 303 " --> pdb=" O ILE M 292 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA M 294 " --> pdb=" O VAL M 301 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL M 301 " --> pdb=" O LEU M 320 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LEU M 320 " --> pdb=" O VAL M 301 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR M 303 " --> pdb=" O GLU M 318 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1723 1.33 - 1.45: 1024 1.45 - 1.58: 3799 1.58 - 1.70: 0 1.70 - 1.82: 37 Bond restraints: 6583 Sorted by residual: bond pdb=" CA LYS M 277 " pdb=" C LYS M 277 " ideal model delta sigma weight residual 1.522 1.572 -0.049 1.37e-02 5.33e+03 1.30e+01 bond pdb=" N PRO M 77 " pdb=" CD PRO M 77 " ideal model delta sigma weight residual 1.473 1.523 -0.050 1.40e-02 5.10e+03 1.29e+01 bond pdb=" N ASP P 59 " pdb=" CA ASP P 59 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.29e-02 6.01e+03 9.78e+00 bond pdb=" C GLU F 530 " pdb=" N VAL F 531 " ideal model delta sigma weight residual 1.334 1.373 -0.039 1.26e-02 6.30e+03 9.68e+00 bond pdb=" N ILE M 191 " pdb=" CA ILE M 191 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.06e-02 8.90e+03 9.54e+00 ... (remaining 6578 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 8355 2.19 - 4.37: 499 4.37 - 6.56: 95 6.56 - 8.75: 21 8.75 - 10.93: 8 Bond angle restraints: 8978 Sorted by residual: angle pdb=" N MET P 58 " pdb=" CA MET P 58 " pdb=" C MET P 58 " ideal model delta sigma weight residual 113.72 102.79 10.93 1.30e+00 5.92e-01 7.07e+01 angle pdb=" N MET Q 58 " pdb=" CA MET Q 58 " pdb=" C MET Q 58 " ideal model delta sigma weight residual 111.02 121.21 -10.19 1.22e+00 6.72e-01 6.98e+01 angle pdb=" N LEU Q 78 " pdb=" CA LEU Q 78 " pdb=" C LEU Q 78 " ideal model delta sigma weight residual 111.11 120.40 -9.29 1.20e+00 6.94e-01 5.99e+01 angle pdb=" N ILE P 60 " pdb=" CA ILE P 60 " pdb=" C ILE P 60 " ideal model delta sigma weight residual 108.96 117.33 -8.37 1.09e+00 8.42e-01 5.90e+01 angle pdb=" N ASP N 116 " pdb=" CA ASP N 116 " pdb=" C ASP N 116 " ideal model delta sigma weight residual 111.71 101.52 10.19 1.34e+00 5.57e-01 5.78e+01 ... (remaining 8973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3676 17.94 - 35.87: 271 35.87 - 53.81: 55 53.81 - 71.74: 12 71.74 - 89.68: 7 Dihedral angle restraints: 4021 sinusoidal: 1352 harmonic: 2669 Sorted by residual: dihedral pdb=" CA LEU M 302 " pdb=" C LEU M 302 " pdb=" N THR M 303 " pdb=" CA THR M 303 " ideal model delta harmonic sigma weight residual 180.00 160.83 19.17 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" N ARG Q 72 " pdb=" C ARG Q 72 " pdb=" CA ARG Q 72 " pdb=" CB ARG Q 72 " ideal model delta harmonic sigma weight residual 122.80 114.10 8.70 0 2.50e+00 1.60e-01 1.21e+01 dihedral pdb=" CA ASP N 124 " pdb=" CB ASP N 124 " pdb=" CG ASP N 124 " pdb=" OD1 ASP N 124 " ideal model delta sinusoidal sigma weight residual -30.00 -89.20 59.20 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 4018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 892 0.084 - 0.169: 172 0.169 - 0.253: 43 0.253 - 0.337: 5 0.337 - 0.421: 1 Chirality restraints: 1113 Sorted by residual: chirality pdb=" CA LEU Q 78 " pdb=" N LEU Q 78 " pdb=" C LEU Q 78 " pdb=" CB LEU Q 78 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" CA TRP M 246 " pdb=" N TRP M 246 " pdb=" C TRP M 246 " pdb=" CB TRP M 246 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA MET P 58 " pdb=" N MET P 58 " pdb=" C MET P 58 " pdb=" CB MET P 58 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 1110 not shown) Planarity restraints: 1192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU N 89 " -0.024 2.00e-02 2.50e+03 4.86e-02 2.36e+01 pdb=" C LEU N 89 " 0.084 2.00e-02 2.50e+03 pdb=" O LEU N 89 " -0.031 2.00e-02 2.50e+03 pdb=" N ASP N 90 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR P 74 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.80e+00 pdb=" C THR P 74 " -0.048 2.00e-02 2.50e+03 pdb=" O THR P 74 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE P 75 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 136 " -0.243 9.50e-02 1.11e+02 1.09e-01 7.26e+00 pdb=" NE ARG M 136 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG M 136 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG M 136 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG M 136 " -0.009 2.00e-02 2.50e+03 ... (remaining 1189 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 2361 2.87 - 3.38: 6391 3.38 - 3.89: 10183 3.89 - 4.39: 10755 4.39 - 4.90: 18285 Nonbonded interactions: 47975 Sorted by model distance: nonbonded pdb=" O GLN Q 108 " pdb=" OG1 THR Q 123 " model vdw 2.368 3.040 nonbonded pdb=" OD1 ASP G 120 " pdb=" NH1 ARG G 123 " model vdw 2.384 3.120 nonbonded pdb=" O GLN P 108 " pdb=" OG1 THR P 123 " model vdw 2.419 3.040 nonbonded pdb=" N LEU N 89 " pdb=" O LEU N 89 " model vdw 2.438 2.496 nonbonded pdb=" OD1 ASN G 187 " pdb=" N LYS G 189 " model vdw 2.456 3.120 ... (remaining 47970 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'N' and (resid 53 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 74 or (resid 75 and (name N or nam \ e CA or name C or name O or name CB )) or resid 76 through 135)) selection = (chain 'P' and (resid 53 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )) or resid 56 through 59 or (resid 60 and (name N or nam \ e CA or name C or name O or name CB )) or resid 61 through 135)) selection = (chain 'Q' and (resid 53 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )) or resid 56 through 74 or (resid 75 and (name N or nam \ e CA or name C or name O or name CB )) or resid 76 through 132 or (resid 133 and \ (name N or name CA or name C or name O or name CB )) or resid 134 through 135)) \ } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 580.710 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 30.410 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 626.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2769 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 : 0.007 0.050 6583 Z= 0.461 Angle : 1.155 10.933 8978 Z= 0.808 Chirality : 0.072 0.421 1113 Planarity : 0.006 0.109 1192 Dihedral : 14.031 89.679 2283 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.17 % Allowed : 17.96 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % 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: 1.06 (0.29), residues: 913 helix: 1.99 (0.25), residues: 442 sheet: -0.20 (0.57), residues: 73 loop : -0.58 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 246 HIS 0.002 0.001 HIS M 90 PHE 0.010 0.001 PHE M 215 TYR 0.007 0.001 TYR M 306 ARG 0.007 0.001 ARG Q 70 Details of bonding type rmsd hydrogen bonds : bond 0.16225 ( 403) hydrogen bonds : angle 6.65464 ( 1176) covalent geometry : bond 0.00658 ( 6583) covalent geometry : angle 1.15515 ( 8978) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 2 residues processed: 193 average time/residue: 1.2545 time to fit residues: 253.8527 Evaluate side-chains 102 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 149 PHE Chi-restraints excluded: chain M residue 155 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 37 optimal weight: 0.2980 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 36 optimal weight: 0.0470 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.0020 chunk 52 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.3086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.105032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.082054 restraints weight = 20277.883| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.42 r_work: 0.3449 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3705 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6583 Z= 0.161 Angle : 0.732 9.791 8978 Z= 0.359 Chirality : 0.045 0.162 1113 Planarity : 0.005 0.081 1192 Dihedral : 4.129 30.306 986 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.87 % Allowed : 24.53 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % 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: 1.25 (0.29), residues: 913 helix: 2.19 (0.25), residues: 444 sheet: 0.17 (0.56), residues: 75 loop : -0.63 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP M 246 HIS 0.003 0.001 HIS G 126 PHE 0.014 0.001 PHE M 124 TYR 0.007 0.001 TYR P 104 ARG 0.007 0.001 ARG P 131 Details of bonding type rmsd hydrogen bonds : bond 0.03417 ( 403) hydrogen bonds : angle 4.74946 ( 1176) covalent geometry : bond 0.00354 ( 6583) covalent geometry : angle 0.73242 ( 8978) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 107 ILE cc_start: 0.6892 (mt) cc_final: 0.6587 (mp) REVERT: G 150 ASP cc_start: 0.6431 (OUTLIER) cc_final: 0.6173 (p0) REVERT: G 174 GLU cc_start: 0.6558 (tp30) cc_final: 0.5903 (tm-30) REVERT: G 177 GLU cc_start: 0.6288 (tp30) cc_final: 0.5529 (tm-30) REVERT: G 188 LEU cc_start: 0.7970 (pt) cc_final: 0.7308 (tt) REVERT: G 227 GLN cc_start: 0.8595 (tp40) cc_final: 0.8338 (tp40) REVERT: M 224 ILE cc_start: 0.5639 (OUTLIER) cc_final: 0.4827 (mt) REVERT: N 77 GLU cc_start: 0.7607 (pm20) cc_final: 0.7319 (pm20) REVERT: P 77 GLU cc_start: 0.4481 (OUTLIER) cc_final: 0.4207 (mt-10) REVERT: P 114 VAL cc_start: 0.5527 (OUTLIER) cc_final: 0.5220 (t) REVERT: P 116 ASP cc_start: 0.6347 (t0) cc_final: 0.6135 (t0) REVERT: Q 118 TYR cc_start: 0.5718 (m-10) cc_final: 0.5079 (m-10) outliers start: 34 outliers final: 6 residues processed: 156 average time/residue: 1.2033 time to fit residues: 201.8598 Evaluate side-chains 115 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain M residue 155 ASN Chi-restraints excluded: chain M residue 194 SER Chi-restraints excluded: chain M residue 224 ILE Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain Q residue 71 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.0570 chunk 84 optimal weight: 0.0770 chunk 70 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 89 optimal weight: 0.0970 chunk 54 optimal weight: 0.3980 chunk 36 optimal weight: 0.4980 chunk 12 optimal weight: 30.0000 chunk 33 optimal weight: 6.9990 chunk 71 optimal weight: 0.0270 chunk 45 optimal weight: 0.9990 overall best weight: 0.1312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 106 HIS M 312 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.105786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.084413 restraints weight = 20770.194| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.40 r_work: 0.3508 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3908 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6583 Z= 0.130 Angle : 0.691 9.460 8978 Z= 0.332 Chirality : 0.044 0.152 1113 Planarity : 0.005 0.075 1192 Dihedral : 3.855 25.843 984 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.84 % Allowed : 26.94 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % 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: 1.28 (0.29), residues: 913 helix: 2.21 (0.25), residues: 445 sheet: 0.37 (0.54), residues: 81 loop : -0.68 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 169 HIS 0.006 0.001 HIS G 126 PHE 0.026 0.002 PHE G 149 TYR 0.006 0.001 TYR P 104 ARG 0.009 0.001 ARG Q 80 Details of bonding type rmsd hydrogen bonds : bond 0.03120 ( 403) hydrogen bonds : angle 4.49244 ( 1176) covalent geometry : bond 0.00293 ( 6583) covalent geometry : angle 0.69144 ( 8978) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 146 LEU cc_start: 0.5708 (tt) cc_final: 0.5127 (tp) REVERT: G 150 ASP cc_start: 0.6852 (OUTLIER) cc_final: 0.6632 (p0) REVERT: G 174 GLU cc_start: 0.6733 (tp30) cc_final: 0.5838 (tt0) REVERT: G 177 GLU cc_start: 0.6356 (tp30) cc_final: 0.5607 (tm-30) REVERT: G 188 LEU cc_start: 0.7881 (pt) cc_final: 0.7073 (tt) REVERT: G 193 MET cc_start: 0.2529 (mpp) cc_final: 0.1933 (tpp) REVERT: M 184 MET cc_start: 0.1493 (pmm) cc_final: -0.1157 (tpp) REVERT: M 249 ASN cc_start: 0.5484 (m-40) cc_final: 0.5253 (p0) REVERT: M 306 TYR cc_start: 0.3132 (OUTLIER) cc_final: 0.1419 (p90) REVERT: N 77 GLU cc_start: 0.7522 (pm20) cc_final: 0.6990 (pm20) REVERT: P 102 ASN cc_start: 0.4946 (t0) cc_final: 0.4485 (t0) REVERT: Q 73 MET cc_start: 0.2418 (pmm) cc_final: 0.2069 (pmm) REVERT: Q 118 TYR cc_start: 0.5956 (m-10) cc_final: 0.5458 (m-10) outliers start: 28 outliers final: 5 residues processed: 134 average time/residue: 1.1055 time to fit residues: 158.7194 Evaluate side-chains 106 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain M residue 306 TYR Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain P residue 70 ARG Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain P residue 120 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 70 optimal weight: 3.9990 chunk 22 optimal weight: 0.0270 chunk 48 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 60 optimal weight: 0.0980 overall best weight: 0.3038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN M 106 HIS Q 108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.107797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.086489 restraints weight = 21919.552| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 3.60 r_work: 0.3573 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4662 moved from start: 0.7058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 6583 Z= 0.158 Angle : 0.740 12.066 8978 Z= 0.357 Chirality : 0.046 0.222 1113 Planarity : 0.005 0.079 1192 Dihedral : 3.822 15.777 982 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.01 % Allowed : 26.94 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % 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: 1.25 (0.29), residues: 913 helix: 2.23 (0.25), residues: 442 sheet: 0.36 (0.53), residues: 92 loop : -0.77 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 169 HIS 0.007 0.001 HIS M 148 PHE 0.026 0.002 PHE G 149 TYR 0.035 0.002 TYR Q 104 ARG 0.007 0.001 ARG M 94 Details of bonding type rmsd hydrogen bonds : bond 0.03214 ( 403) hydrogen bonds : angle 4.54500 ( 1176) covalent geometry : bond 0.00370 ( 6583) covalent geometry : angle 0.74028 ( 8978) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 107 ILE cc_start: 0.7422 (mp) cc_final: 0.7212 (tp) REVERT: G 174 GLU cc_start: 0.7728 (tp30) cc_final: 0.6583 (tt0) REVERT: G 177 GLU cc_start: 0.7221 (tp30) cc_final: 0.6634 (tm-30) REVERT: M 121 SER cc_start: 0.5776 (m) cc_final: 0.5267 (t) REVERT: M 165 TYR cc_start: 0.3200 (t80) cc_final: 0.2811 (t80) REVERT: M 184 MET cc_start: 0.3621 (pmm) cc_final: 0.2520 (mtp) REVERT: M 249 ASN cc_start: 0.5908 (m-40) cc_final: 0.5364 (p0) REVERT: M 306 TYR cc_start: 0.3928 (OUTLIER) cc_final: 0.2048 (p90) REVERT: M 321 ILE cc_start: 0.6413 (mt) cc_final: 0.6004 (tt) REVERT: N 110 GLU cc_start: 0.6528 (tp30) cc_final: 0.6111 (tp30) REVERT: P 70 ARG cc_start: 0.2930 (OUTLIER) cc_final: 0.2171 (mpt-90) REVERT: P 102 ASN cc_start: 0.5951 (t0) cc_final: 0.5713 (m110) REVERT: Q 101 ILE cc_start: 0.2504 (OUTLIER) cc_final: 0.2011 (mp) REVERT: Q 113 VAL cc_start: 0.6495 (OUTLIER) cc_final: 0.6291 (m) outliers start: 29 outliers final: 7 residues processed: 177 average time/residue: 0.9356 time to fit residues: 176.9223 Evaluate side-chains 148 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 155 ASN Chi-restraints excluded: chain M residue 194 SER Chi-restraints excluded: chain M residue 306 TYR Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain P residue 70 ARG Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 101 ILE Chi-restraints excluded: chain Q residue 113 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 31 optimal weight: 1.9990 chunk 63 optimal weight: 0.0870 chunk 50 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 3 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 89 optimal weight: 0.0670 chunk 23 optimal weight: 0.0170 chunk 6 optimal weight: 0.0000 overall best weight: 0.1538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.109601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.089934 restraints weight = 22209.764| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 3.97 r_work: 0.3605 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4904 moved from start: 0.8010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6583 Z= 0.130 Angle : 0.748 11.659 8978 Z= 0.353 Chirality : 0.045 0.197 1113 Planarity : 0.005 0.069 1192 Dihedral : 3.760 15.752 982 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.53 % Allowed : 31.78 % Favored : 62.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % 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: 1.24 (0.29), residues: 913 helix: 2.15 (0.26), residues: 450 sheet: 0.39 (0.52), residues: 92 loop : -0.74 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP M 169 HIS 0.005 0.001 HIS M 148 PHE 0.022 0.002 PHE G 149 TYR 0.014 0.002 TYR Q 104 ARG 0.006 0.001 ARG N 121 Details of bonding type rmsd hydrogen bonds : bond 0.02914 ( 403) hydrogen bonds : angle 4.34339 ( 1176) covalent geometry : bond 0.00292 ( 6583) covalent geometry : angle 0.74793 ( 8978) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 149 PHE cc_start: 0.6918 (m-10) cc_final: 0.6463 (m-10) REVERT: G 158 MET cc_start: 0.6511 (mmp) cc_final: 0.6295 (mmt) REVERT: G 174 GLU cc_start: 0.8042 (tp30) cc_final: 0.7256 (mm-30) REVERT: G 177 GLU cc_start: 0.7333 (tp30) cc_final: 0.6679 (tm-30) REVERT: G 183 LEU cc_start: 0.6310 (OUTLIER) cc_final: 0.6068 (tt) REVERT: G 193 MET cc_start: 0.3663 (mmt) cc_final: 0.3156 (tpt) REVERT: M 67 MET cc_start: 0.6836 (tmm) cc_final: 0.6525 (tmm) REVERT: M 121 SER cc_start: 0.6217 (m) cc_final: 0.5664 (t) REVERT: M 184 MET cc_start: 0.3757 (pmm) cc_final: 0.2675 (mtp) REVERT: M 249 ASN cc_start: 0.6192 (m-40) cc_final: 0.5508 (p0) REVERT: M 268 ILE cc_start: 0.6157 (mm) cc_final: 0.5829 (mm) REVERT: M 306 TYR cc_start: 0.3806 (OUTLIER) cc_final: 0.1697 (p90) REVERT: N 54 ILE cc_start: 0.6046 (mt) cc_final: 0.5837 (mm) REVERT: P 102 ASN cc_start: 0.6702 (t0) cc_final: 0.6389 (m110) outliers start: 32 outliers final: 12 residues processed: 162 average time/residue: 0.7334 time to fit residues: 128.0956 Evaluate side-chains 146 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 155 ASN Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain M residue 306 TYR Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 70 ARG Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 44 optimal weight: 0.9980 chunk 53 optimal weight: 0.2980 chunk 55 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 chunk 28 optimal weight: 7.9990 chunk 84 optimal weight: 0.5980 chunk 51 optimal weight: 0.3980 chunk 79 optimal weight: 0.3980 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 87 GLN ** Q 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.111864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.091919 restraints weight = 23040.872| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 3.77 r_work: 0.3688 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6227 moved from start: 1.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 6583 Z= 0.205 Angle : 0.878 12.773 8978 Z= 0.428 Chirality : 0.052 0.317 1113 Planarity : 0.006 0.071 1192 Dihedral : 4.228 18.057 982 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 7.77 % Allowed : 30.40 % Favored : 61.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % 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: 0.95 (0.28), residues: 913 helix: 1.95 (0.26), residues: 449 sheet: 0.30 (0.57), residues: 73 loop : -0.90 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP M 169 HIS 0.009 0.002 HIS M 148 PHE 0.021 0.003 PHE M 118 TYR 0.014 0.002 TYR N 118 ARG 0.013 0.001 ARG G 154 Details of bonding type rmsd hydrogen bonds : bond 0.03910 ( 403) hydrogen bonds : angle 4.80561 ( 1176) covalent geometry : bond 0.00501 ( 6583) covalent geometry : angle 0.87816 ( 8978) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 161 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 174 GLU cc_start: 0.8672 (tp30) cc_final: 0.8184 (tp30) REVERT: G 227 GLN cc_start: 0.8656 (tp40) cc_final: 0.8428 (tp40) REVERT: M 67 MET cc_start: 0.7815 (tmm) cc_final: 0.7580 (tmm) REVERT: M 186 VAL cc_start: 0.8957 (t) cc_final: 0.8742 (p) REVERT: M 306 TYR cc_start: 0.3749 (OUTLIER) cc_final: 0.2043 (p90) REVERT: M 321 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.7944 (pp) REVERT: N 54 ILE cc_start: 0.6165 (mt) cc_final: 0.5864 (mm) REVERT: N 78 LEU cc_start: 0.8574 (tm) cc_final: 0.8373 (tt) REVERT: N 92 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8374 (tm) REVERT: N 95 GLU cc_start: 0.6415 (OUTLIER) cc_final: 0.5969 (pm20) REVERT: Q 52 GLN cc_start: -0.1121 (OUTLIER) cc_final: -0.1345 (pm20) REVERT: Q 126 ILE cc_start: 0.4905 (OUTLIER) cc_final: 0.3897 (tp) outliers start: 45 outliers final: 14 residues processed: 185 average time/residue: 0.9200 time to fit residues: 180.6611 Evaluate side-chains 143 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 182 SER Chi-restraints excluded: chain M residue 306 TYR Chi-restraints excluded: chain M residue 321 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 95 GLU Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 70 ARG Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 118 TYR Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 126 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 0.0370 chunk 85 optimal weight: 0.3980 chunk 69 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 68 optimal weight: 0.2980 chunk 20 optimal weight: 0.0170 chunk 14 optimal weight: 0.4980 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.110375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.089677 restraints weight = 23232.106| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 3.83 r_work: 0.3661 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 1.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6583 Z= 0.151 Angle : 0.841 12.944 8978 Z= 0.397 Chirality : 0.048 0.246 1113 Planarity : 0.005 0.059 1192 Dihedral : 3.924 20.939 982 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.49 % Allowed : 37.82 % Favored : 57.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % 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: 1.12 (0.29), residues: 913 helix: 2.04 (0.26), residues: 450 sheet: 0.75 (0.59), residues: 63 loop : -0.79 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 169 HIS 0.004 0.001 HIS M 256 PHE 0.009 0.001 PHE G 149 TYR 0.014 0.002 TYR P 118 ARG 0.006 0.001 ARG P 80 Details of bonding type rmsd hydrogen bonds : bond 0.03017 ( 403) hydrogen bonds : angle 4.44711 ( 1176) covalent geometry : bond 0.00362 ( 6583) covalent geometry : angle 0.84144 ( 8978) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 174 GLU cc_start: 0.8647 (tp30) cc_final: 0.8101 (tp30) REVERT: G 177 GLU cc_start: 0.8560 (tp30) cc_final: 0.8071 (tt0) REVERT: G 227 GLN cc_start: 0.8669 (tp40) cc_final: 0.8396 (tp40) REVERT: M 67 MET cc_start: 0.8030 (tmm) cc_final: 0.7759 (tmm) REVERT: M 194 SER cc_start: 0.8440 (t) cc_final: 0.8012 (t) REVERT: M 297 ASP cc_start: 0.7682 (p0) cc_final: 0.7161 (t0) REVERT: M 306 TYR cc_start: 0.3903 (OUTLIER) cc_final: 0.2218 (p90) REVERT: N 54 ILE cc_start: 0.6240 (mt) cc_final: 0.6017 (mm) REVERT: N 92 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8406 (tm) REVERT: N 95 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6328 (pm20) REVERT: Q 111 VAL cc_start: 0.8897 (p) cc_final: 0.8615 (p) outliers start: 26 outliers final: 5 residues processed: 167 average time/residue: 0.7219 time to fit residues: 129.8145 Evaluate side-chains 129 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 306 TYR Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 95 GLU Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 118 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 48 optimal weight: 0.5980 chunk 17 optimal weight: 0.0970 chunk 36 optimal weight: 0.0970 chunk 10 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 44 optimal weight: 0.0060 chunk 68 optimal weight: 0.0670 overall best weight: 0.1730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 128 GLN M 87 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.110559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.088855 restraints weight = 23193.657| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 3.85 r_work: 0.3651 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 1.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6583 Z= 0.149 Angle : 0.866 11.833 8978 Z= 0.404 Chirality : 0.048 0.253 1113 Planarity : 0.005 0.063 1192 Dihedral : 3.949 23.618 982 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.63 % Allowed : 41.28 % Favored : 55.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % 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: 0.98 (0.29), residues: 913 helix: 1.87 (0.26), residues: 449 sheet: 0.60 (0.61), residues: 61 loop : -0.75 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 169 HIS 0.004 0.001 HIS G 126 PHE 0.011 0.001 PHE M 61 TYR 0.014 0.002 TYR N 118 ARG 0.009 0.001 ARG P 70 Details of bonding type rmsd hydrogen bonds : bond 0.02824 ( 403) hydrogen bonds : angle 4.45641 ( 1176) covalent geometry : bond 0.00352 ( 6583) covalent geometry : angle 0.86576 ( 8978) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 174 GLU cc_start: 0.8690 (tp30) cc_final: 0.8214 (tp30) REVERT: G 177 GLU cc_start: 0.8652 (tp30) cc_final: 0.8016 (tt0) REVERT: M 67 MET cc_start: 0.8181 (tmm) cc_final: 0.7941 (tmm) REVERT: M 297 ASP cc_start: 0.7821 (p0) cc_final: 0.7397 (t0) REVERT: M 306 TYR cc_start: 0.3914 (OUTLIER) cc_final: 0.2032 (p90) REVERT: N 54 ILE cc_start: 0.6352 (mt) cc_final: 0.6104 (mm) REVERT: N 62 VAL cc_start: 0.8822 (m) cc_final: 0.8404 (m) REVERT: N 92 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8451 (tm) REVERT: N 95 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6540 (pm20) REVERT: P 73 MET cc_start: 0.7391 (tpp) cc_final: 0.7141 (ttm) REVERT: Q 62 VAL cc_start: 0.6952 (t) cc_final: 0.6549 (t) REVERT: Q 65 THR cc_start: 0.7307 (p) cc_final: 0.7045 (p) REVERT: Q 75 ILE cc_start: -0.0918 (OUTLIER) cc_final: -0.1430 (mm) REVERT: Q 92 LEU cc_start: 0.7348 (pp) cc_final: 0.7075 (pp) outliers start: 21 outliers final: 9 residues processed: 148 average time/residue: 0.8011 time to fit residues: 127.1469 Evaluate side-chains 132 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 306 TYR Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 95 GLU Chi-restraints excluded: chain P residue 60 ILE Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 118 TYR Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 75 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 89 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 39 optimal weight: 0.0570 chunk 31 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 15 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 58 ASN ** M 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 264 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.106675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.082648 restraints weight = 23458.858| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 3.88 r_work: 0.3516 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 1.6459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 6583 Z= 0.213 Angle : 1.032 18.966 8978 Z= 0.498 Chirality : 0.053 0.247 1113 Planarity : 0.006 0.074 1192 Dihedral : 4.760 22.592 982 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.66 % Allowed : 41.28 % Favored : 54.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % 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: 0.76 (0.28), residues: 913 helix: 1.70 (0.26), residues: 444 sheet: 0.06 (0.60), residues: 72 loop : -0.79 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP M 169 HIS 0.006 0.002 HIS M 256 PHE 0.026 0.003 PHE M 61 TYR 0.022 0.003 TYR P 118 ARG 0.013 0.001 ARG G 123 Details of bonding type rmsd hydrogen bonds : bond 0.03571 ( 403) hydrogen bonds : angle 4.85564 ( 1176) covalent geometry : bond 0.00514 ( 6583) covalent geometry : angle 1.03168 ( 8978) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 120 ASP cc_start: 0.7829 (m-30) cc_final: 0.7126 (t0) REVERT: G 150 ASP cc_start: 0.7804 (p0) cc_final: 0.7577 (p0) REVERT: G 152 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7775 (ppp80) REVERT: G 177 GLU cc_start: 0.9180 (tp30) cc_final: 0.8938 (tt0) REVERT: G 193 MET cc_start: 0.7294 (mmp) cc_final: 0.7069 (ppp) REVERT: G 227 GLN cc_start: 0.8901 (tp40) cc_final: 0.7950 (tp40) REVERT: M 54 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7510 (tp) REVERT: M 170 LYS cc_start: 0.9021 (mmmt) cc_final: 0.8789 (mmmt) REVERT: M 205 HIS cc_start: 0.8135 (t-90) cc_final: 0.7913 (t-90) REVERT: M 297 ASP cc_start: 0.8149 (p0) cc_final: 0.7937 (t0) REVERT: M 301 VAL cc_start: 0.9453 (t) cc_final: 0.9222 (m) REVERT: M 306 TYR cc_start: 0.4489 (OUTLIER) cc_final: 0.2732 (p90) REVERT: N 54 ILE cc_start: 0.7084 (mt) cc_final: 0.6798 (mm) REVERT: N 64 LEU cc_start: 0.9300 (mp) cc_final: 0.9058 (pp) REVERT: N 92 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8466 (tm) REVERT: N 110 GLU cc_start: 0.6944 (tp30) cc_final: 0.6736 (tp30) REVERT: P 60 ILE cc_start: 0.6223 (OUTLIER) cc_final: 0.5994 (pp) REVERT: P 67 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7756 (tm-30) REVERT: P 99 ILE cc_start: 0.8902 (mm) cc_final: 0.8612 (mp) REVERT: Q 123 THR cc_start: 0.9185 (m) cc_final: 0.8848 (p) outliers start: 27 outliers final: 8 residues processed: 164 average time/residue: 0.9858 time to fit residues: 170.8359 Evaluate side-chains 130 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 152 ARG Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 292 ILE Chi-restraints excluded: chain M residue 306 TYR Chi-restraints excluded: chain M residue 308 THR Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain P residue 60 ILE Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 118 TYR Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 124 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 25 optimal weight: 0.9990 chunk 64 optimal weight: 0.0000 chunk 88 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 77 optimal weight: 0.0050 chunk 72 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 11 optimal weight: 30.0000 chunk 62 optimal weight: 0.0980 chunk 67 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 58 ASN ** M 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.106058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.081932 restraints weight = 23524.371| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 3.87 r_work: 0.3505 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 1.6919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6583 Z= 0.168 Angle : 0.987 20.043 8978 Z= 0.458 Chirality : 0.049 0.305 1113 Planarity : 0.005 0.063 1192 Dihedral : 4.415 27.884 982 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.94 % Allowed : 46.11 % Favored : 50.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % 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: 0.88 (0.28), residues: 913 helix: 1.81 (0.26), residues: 451 sheet: 0.10 (0.56), residues: 77 loop : -0.79 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 169 HIS 0.003 0.001 HIS M 295 PHE 0.015 0.001 PHE G 149 TYR 0.014 0.002 TYR P 104 ARG 0.015 0.001 ARG P 70 Details of bonding type rmsd hydrogen bonds : bond 0.02972 ( 403) hydrogen bonds : angle 4.65850 ( 1176) covalent geometry : bond 0.00406 ( 6583) covalent geometry : angle 0.98722 ( 8978) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 108 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8116 (mm-30) REVERT: G 120 ASP cc_start: 0.8140 (m-30) cc_final: 0.7508 (t0) REVERT: G 152 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7963 (ppp80) REVERT: G 174 GLU cc_start: 0.8735 (tp30) cc_final: 0.8521 (tp30) REVERT: G 177 GLU cc_start: 0.9181 (tp30) cc_final: 0.8888 (tt0) REVERT: G 193 MET cc_start: 0.7439 (mmp) cc_final: 0.7205 (ppp) REVERT: G 227 GLN cc_start: 0.8611 (tp40) cc_final: 0.8330 (tp40) REVERT: M 67 MET cc_start: 0.8691 (tmm) cc_final: 0.8228 (tmm) REVERT: M 205 HIS cc_start: 0.7809 (t70) cc_final: 0.7521 (t-90) REVERT: M 301 VAL cc_start: 0.9522 (t) cc_final: 0.9287 (m) REVERT: M 306 TYR cc_start: 0.4634 (OUTLIER) cc_final: 0.2690 (p90) REVERT: N 64 LEU cc_start: 0.9408 (mp) cc_final: 0.8951 (pp) REVERT: N 77 GLU cc_start: 0.8903 (mp0) cc_final: 0.8392 (pm20) REVERT: N 79 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8169 (mm) REVERT: N 110 GLU cc_start: 0.7087 (tp30) cc_final: 0.6837 (tp30) REVERT: N 130 GLU cc_start: 0.6551 (tm-30) cc_final: 0.6262 (pp20) REVERT: P 97 LEU cc_start: 0.6072 (mm) cc_final: 0.5870 (mm) REVERT: Q 73 MET cc_start: 0.6173 (pmm) cc_final: 0.4923 (ptp) REVERT: Q 123 THR cc_start: 0.9192 (m) cc_final: 0.8938 (p) REVERT: Q 132 MET cc_start: 0.8252 (mmt) cc_final: 0.7995 (mpm) outliers start: 17 outliers final: 9 residues processed: 147 average time/residue: 1.5076 time to fit residues: 233.7536 Evaluate side-chains 123 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 152 ARG Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 306 TYR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain P residue 60 ILE Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 118 TYR Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 124 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 81 optimal weight: 0.5980 chunk 82 optimal weight: 0.3980 chunk 27 optimal weight: 20.0000 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 40.0000 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 205 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.099971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.076067 restraints weight = 22803.241| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 4.12 r_work: 0.3313 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 1.8315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 6583 Z= 0.226 Angle : 1.036 17.453 8978 Z= 0.492 Chirality : 0.050 0.197 1113 Planarity : 0.006 0.067 1192 Dihedral : 4.686 21.857 982 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.28 % Allowed : 46.46 % Favored : 50.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % 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: 0.87 (0.28), residues: 913 helix: 1.73 (0.26), residues: 451 sheet: 0.28 (0.61), residues: 67 loop : -0.72 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP M 169 HIS 0.005 0.001 HIS G 136 PHE 0.027 0.003 PHE M 61 TYR 0.015 0.002 TYR N 118 ARG 0.024 0.001 ARG Q 121 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 403) hydrogen bonds : angle 4.77993 ( 1176) covalent geometry : bond 0.00554 ( 6583) covalent geometry : angle 1.03646 ( 8978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10306.63 seconds wall clock time: 182 minutes 14.47 seconds (10934.47 seconds total)