Starting phenix.real_space_refine on Wed Sep 17 07:08:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n49_48871/09_2025/9n49_48871.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n49_48871/09_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_48871/09_2025/9n49_48871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n49_48871/09_2025/9n49_48871.map" model { file = "/net/cci-nas-00/data/ceres_data/9n49_48871/09_2025/9n49_48871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n49_48871/09_2025/9n49_48871.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 4, 'GLU:plan': 3, 'GLN:plan1': 6, 'ARG:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1} 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: {'ASP:plan': 12, 'GLU:plan': 21, 'ARG:plan': 16, 'PHE:plan': 6, 'HIS:plan': 1, 'GLN:plan1': 11, 'ASN:plan1': 9, 'TYR:plan': 1} 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, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 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: {'ASP:plan': 1, 'ARG: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: 1.89, per 1000 atoms: 0.29 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: 0.50 Conformation dependent library (CDL) restraints added in 425.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.26 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: 1.04 Time building geometry restraints manager: 0.71 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: 40.950 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.500 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.300 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (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 ARG 0.007 0.001 ARG Q 70 TYR 0.007 0.001 TYR M 306 PHE 0.010 0.001 PHE M 215 TRP 0.006 0.001 TRP M 246 HIS 0.002 0.001 HIS M 90 Details of bonding type rmsd covalent geometry : bond 0.00658 ( 6583) covalent geometry : angle 1.15515 ( 8978) hydrogen bonds : bond 0.16225 ( 403) hydrogen bonds : angle 6.65464 ( 1176) *********************** 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 : 0.274 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: 0.6181 time to fit residues: 124.6286 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 : 0.299 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.0070 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 overall best weight: 0.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 111 ASN M 245 ASN ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.105277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.082144 restraints weight = 20487.529| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.46 r_work: 0.3451 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3771 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6583 Z= 0.151 Angle : 0.743 9.587 8978 Z= 0.362 Chirality : 0.045 0.150 1113 Planarity : 0.005 0.073 1192 Dihedral : 4.209 31.193 986 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.87 % Allowed : 23.83 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.28), residues: 913 helix: 2.17 (0.25), residues: 442 sheet: 0.49 (0.59), residues: 65 loop : -0.59 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 131 TYR 0.008 0.001 TYR M 165 PHE 0.014 0.002 PHE M 124 TRP 0.003 0.001 TRP M 246 HIS 0.003 0.001 HIS M 148 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6583) covalent geometry : angle 0.74251 ( 8978) hydrogen bonds : bond 0.03427 ( 403) hydrogen bonds : angle 4.70689 ( 1176) *********************** 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 165 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.262 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 107 ILE cc_start: 0.7200 (mt) cc_final: 0.6926 (mp) REVERT: G 113 MET cc_start: 0.2348 (tpt) cc_final: 0.1766 (tmm) REVERT: G 150 ASP cc_start: 0.6501 (OUTLIER) cc_final: 0.6192 (p0) REVERT: G 174 GLU cc_start: 0.6629 (tp30) cc_final: 0.5925 (tm-30) REVERT: G 177 GLU cc_start: 0.6351 (tp30) cc_final: 0.5571 (tm-30) REVERT: G 193 MET cc_start: 0.3556 (mpp) cc_final: 0.3216 (tpp) REVERT: G 227 GLN cc_start: 0.8564 (tp40) cc_final: 0.8325 (tp40) REVERT: M 184 MET cc_start: 0.1627 (pmm) cc_final: -0.1287 (tpp) REVERT: M 224 ILE cc_start: 0.5682 (OUTLIER) cc_final: 0.4904 (mt) REVERT: N 77 GLU cc_start: 0.7719 (pm20) cc_final: 0.7409 (pm20) REVERT: P 114 VAL cc_start: 0.5593 (OUTLIER) cc_final: 0.5289 (t) REVERT: P 116 ASP cc_start: 0.6452 (t0) cc_final: 0.6247 (t0) REVERT: Q 76 LYS cc_start: 0.7859 (mmmt) cc_final: 0.6921 (mmmt) REVERT: Q 118 TYR cc_start: 0.5803 (m-10) cc_final: 0.5176 (m-10) outliers start: 34 outliers final: 7 residues processed: 158 average time/residue: 0.4385 time to fit residues: 73.7345 Evaluate side-chains 122 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 27 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 20.0000 chunk 40 optimal weight: 0.5980 chunk 86 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 111 ASN ** M 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 264 ASN M 312 GLN P 108 GLN Q 108 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.111116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.090771 restraints weight = 22591.870| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 3.75 r_work: 0.3670 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5790 moved from start: 0.9480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.132 6583 Z= 0.319 Angle : 0.967 13.233 8978 Z= 0.492 Chirality : 0.055 0.237 1113 Planarity : 0.007 0.082 1192 Dihedral : 5.233 45.295 984 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 6.91 % Allowed : 24.70 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.28), residues: 913 helix: 1.78 (0.25), residues: 441 sheet: 0.02 (0.53), residues: 92 loop : -1.06 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG Q 80 TYR 0.027 0.003 TYR Q 104 PHE 0.029 0.004 PHE M 124 TRP 0.008 0.002 TRP M 246 HIS 0.012 0.002 HIS M 148 Details of bonding type rmsd covalent geometry : bond 0.00632 ( 6583) covalent geometry : angle 0.96666 ( 8978) hydrogen bonds : bond 0.04785 ( 403) hydrogen bonds : angle 5.43881 ( 1176) *********************** 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 233 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 193 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 109 THR cc_start: 0.7210 (OUTLIER) cc_final: 0.6745 (m) REVERT: G 227 GLN cc_start: 0.8662 (tp40) cc_final: 0.8120 (tp40) REVERT: G 231 ASP cc_start: 0.7581 (m-30) cc_final: 0.7201 (m-30) REVERT: M 184 MET cc_start: 0.6500 (pmm) cc_final: 0.6115 (mtp) REVERT: M 192 THR cc_start: 0.7850 (OUTLIER) cc_final: 0.7492 (m) REVERT: M 306 TYR cc_start: 0.3911 (OUTLIER) cc_final: 0.2160 (p90) REVERT: N 54 ILE cc_start: 0.6465 (mt) cc_final: 0.6055 (mm) REVERT: N 77 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7523 (mp0) REVERT: N 80 ARG cc_start: 0.5116 (OUTLIER) cc_final: 0.4760 (mmp-170) REVERT: N 110 GLU cc_start: 0.7199 (tp30) cc_final: 0.6972 (mm-30) REVERT: P 102 ASN cc_start: 0.7825 (t0) cc_final: 0.7500 (m-40) REVERT: P 114 VAL cc_start: 0.5342 (OUTLIER) cc_final: 0.5063 (p) REVERT: Q 39 PHE cc_start: 0.3897 (m-80) cc_final: 0.3219 (t80) REVERT: Q 73 MET cc_start: 0.3639 (pmm) cc_final: 0.3250 (pmm) REVERT: Q 118 TYR cc_start: 0.7684 (m-10) cc_final: 0.7420 (m-10) outliers start: 40 outliers final: 7 residues processed: 221 average time/residue: 0.5034 time to fit residues: 117.4677 Evaluate side-chains 145 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 109 THR 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 77 GLU Chi-restraints excluded: chain N residue 80 ARG Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain P residue 70 ARG Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 118 TYR Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain Q residue 100 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 47 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 40 optimal weight: 0.0770 chunk 82 optimal weight: 0.9990 chunk 35 optimal weight: 0.2980 chunk 28 optimal weight: 10.0000 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 95 ASN M 310 ASN ** P 102 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 = 0.4146 r_free = 0.4146 target = 0.108500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.087354 restraints weight = 23234.774| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 3.86 r_work: 0.3601 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 1.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 6583 Z= 0.269 Angle : 0.950 11.119 8978 Z= 0.470 Chirality : 0.052 0.280 1113 Planarity : 0.007 0.085 1192 Dihedral : 4.894 40.077 984 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 7.77 % Allowed : 30.74 % Favored : 61.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.28), residues: 913 helix: 1.72 (0.26), residues: 436 sheet: 0.10 (0.56), residues: 78 loop : -0.94 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 121 TYR 0.018 0.002 TYR N 118 PHE 0.021 0.003 PHE M 92 TRP 0.012 0.002 TRP M 169 HIS 0.008 0.003 HIS M 205 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 6583) covalent geometry : angle 0.94989 ( 8978) hydrogen bonds : bond 0.03876 ( 403) hydrogen bonds : angle 5.09503 ( 1176) *********************** 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 209 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 164 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 124 ASP cc_start: 0.7010 (m-30) cc_final: 0.6309 (t0) REVERT: G 152 ARG cc_start: 0.7829 (tmt170) cc_final: 0.7483 (ptm160) REVERT: G 177 GLU cc_start: 0.8767 (tp30) cc_final: 0.8135 (tt0) REVERT: G 227 GLN cc_start: 0.8843 (tp40) cc_final: 0.8206 (tp40) REVERT: M 67 MET cc_start: 0.8554 (tmm) cc_final: 0.8290 (tmm) REVERT: M 270 LEU cc_start: 0.7908 (mm) cc_final: 0.7701 (mt) REVERT: M 306 TYR cc_start: 0.3740 (OUTLIER) cc_final: 0.1762 (p90) REVERT: N 54 ILE cc_start: 0.6785 (mt) cc_final: 0.6463 (mm) REVERT: N 76 LYS cc_start: 0.6163 (mptt) cc_final: 0.5958 (mptt) REVERT: N 92 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8471 (tm) REVERT: N 95 GLU cc_start: 0.7256 (pm20) cc_final: 0.6789 (pm20) REVERT: P 58 MET cc_start: 0.6405 (mpm) cc_final: 0.6182 (mmm) REVERT: P 65 THR cc_start: 0.6870 (p) cc_final: 0.6335 (t) REVERT: P 67 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6855 (tm-30) REVERT: P 73 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7549 (tmm) REVERT: P 114 VAL cc_start: 0.7234 (OUTLIER) cc_final: 0.6911 (p) REVERT: Q 39 PHE cc_start: 0.5342 (m-80) cc_final: 0.4126 (t80) REVERT: Q 75 ILE cc_start: 0.4070 (mm) cc_final: 0.3046 (mm) outliers start: 45 outliers final: 13 residues processed: 189 average time/residue: 0.4799 time to fit residues: 96.1062 Evaluate side-chains 129 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 154 ARG Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain M residue 84 ILE Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 306 TYR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain P residue 60 ILE Chi-restraints excluded: chain P residue 67 GLU Chi-restraints excluded: chain P residue 73 MET Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 127 THR Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain Q residue 126 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 40.0000 chunk 69 optimal weight: 0.0270 chunk 26 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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** P 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.104916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.080358 restraints weight = 23209.348| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.87 r_work: 0.3463 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 1.5566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6583 Z= 0.182 Angle : 0.814 11.763 8978 Z= 0.389 Chirality : 0.048 0.215 1113 Planarity : 0.006 0.059 1192 Dihedral : 4.263 17.393 982 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.35 % Allowed : 37.13 % Favored : 57.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.29), residues: 913 helix: 2.05 (0.26), residues: 433 sheet: -0.16 (0.57), residues: 83 loop : -0.72 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 85 TYR 0.010 0.001 TYR Q 104 PHE 0.024 0.003 PHE M 61 TRP 0.012 0.002 TRP M 169 HIS 0.006 0.001 HIS M 256 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 6583) covalent geometry : angle 0.81410 ( 8978) hydrogen bonds : bond 0.03233 ( 403) hydrogen bonds : angle 4.54077 ( 1176) *********************** 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 168 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 116 GLN cc_start: 0.7129 (pm20) cc_final: 0.6769 (pp30) REVERT: G 150 ASP cc_start: 0.7726 (t70) cc_final: 0.7265 (p0) REVERT: G 152 ARG cc_start: 0.8134 (tmt170) cc_final: 0.7841 (ppp80) REVERT: G 227 GLN cc_start: 0.8858 (tp40) cc_final: 0.8522 (tp-100) REVERT: G 231 ASP cc_start: 0.7877 (m-30) cc_final: 0.7427 (m-30) REVERT: M 301 VAL cc_start: 0.9430 (t) cc_final: 0.9165 (m) REVERT: M 306 TYR cc_start: 0.4250 (OUTLIER) cc_final: 0.2693 (p90) REVERT: N 54 ILE cc_start: 0.6910 (mt) cc_final: 0.6605 (mm) REVERT: N 73 MET cc_start: 0.6692 (ppp) cc_final: 0.5889 (tmt) REVERT: N 77 GLU cc_start: 0.8906 (mp0) cc_final: 0.8299 (pm20) REVERT: N 92 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8516 (tm) REVERT: P 102 ASN cc_start: 0.8877 (m-40) cc_final: 0.8605 (m-40) REVERT: P 114 VAL cc_start: 0.7457 (OUTLIER) cc_final: 0.7109 (p) REVERT: P 118 TYR cc_start: 0.4354 (OUTLIER) cc_final: 0.3179 (t80) REVERT: Q 39 PHE cc_start: 0.5728 (m-80) cc_final: 0.4605 (t80) REVERT: Q 41 GLN cc_start: 0.8760 (pp30) cc_final: 0.8497 (tp40) REVERT: Q 68 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7242 (mp) REVERT: Q 75 ILE cc_start: 0.4221 (mm) cc_final: 0.2688 (mm) outliers start: 31 outliers final: 6 residues processed: 156 average time/residue: 0.4614 time to fit residues: 75.9669 Evaluate side-chains 126 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 154 ARG Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 306 TYR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain P residue 60 ILE Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 118 TYR Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 68 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 67 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 28 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 89 optimal weight: 0.0770 chunk 70 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.099970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.074689 restraints weight = 22506.416| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.86 r_work: 0.3336 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 1.7678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 6583 Z= 0.192 Angle : 0.861 17.428 8978 Z= 0.412 Chirality : 0.047 0.242 1113 Planarity : 0.005 0.059 1192 Dihedral : 4.419 18.841 982 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.49 % Allowed : 38.17 % Favored : 57.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.29), residues: 913 helix: 1.87 (0.25), residues: 449 sheet: 0.41 (0.61), residues: 60 loop : -0.73 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 121 TYR 0.013 0.002 TYR N 104 PHE 0.019 0.002 PHE M 124 TRP 0.010 0.002 TRP M 169 HIS 0.007 0.001 HIS M 256 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 6583) covalent geometry : angle 0.86060 ( 8978) hydrogen bonds : bond 0.03106 ( 403) hydrogen bonds : angle 4.50061 ( 1176) *********************** 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 163 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 150 ASP cc_start: 0.8181 (t70) cc_final: 0.7763 (p0) REVERT: G 177 GLU cc_start: 0.9240 (tp30) cc_final: 0.9000 (tp30) REVERT: G 202 ILE cc_start: 0.8550 (mm) cc_final: 0.8329 (mp) REVERT: G 227 GLN cc_start: 0.8930 (tp40) cc_final: 0.8543 (tp-100) REVERT: G 231 ASP cc_start: 0.8045 (m-30) cc_final: 0.7478 (m-30) REVERT: M 136 ARG cc_start: 0.6672 (OUTLIER) cc_final: 0.6197 (ptt180) REVERT: M 301 VAL cc_start: 0.9516 (t) cc_final: 0.9308 (m) REVERT: M 306 TYR cc_start: 0.5113 (OUTLIER) cc_final: 0.3115 (p90) REVERT: N 79 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8512 (mm) REVERT: N 92 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8829 (tm) REVERT: N 132 MET cc_start: 0.8670 (mmm) cc_final: 0.8415 (mmm) REVERT: P 58 MET cc_start: 0.7514 (mmm) cc_final: 0.6676 (mmm) REVERT: Q 39 PHE cc_start: 0.7210 (m-80) cc_final: 0.6034 (t80) REVERT: Q 41 GLN cc_start: 0.8907 (pp30) cc_final: 0.8674 (tm-30) REVERT: Q 76 LYS cc_start: 0.7858 (mtmt) cc_final: 0.7172 (mptt) outliers start: 26 outliers final: 4 residues processed: 155 average time/residue: 0.5076 time to fit residues: 83.0009 Evaluate side-chains 112 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 136 ARG Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 306 TYR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain P residue 60 ILE Chi-restraints excluded: chain P residue 114 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 59 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 40 optimal weight: 0.0170 chunk 81 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 75 optimal weight: 0.0010 chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 overall best weight: 0.5224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3972 r_free = 0.3972 target = 0.097817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.071893 restraints weight = 22676.502| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 3.89 r_work: 0.3299 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 1.8406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 6583 Z= 0.169 Angle : 0.843 13.848 8978 Z= 0.397 Chirality : 0.047 0.225 1113 Planarity : 0.005 0.068 1192 Dihedral : 4.246 23.217 982 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.80 % Allowed : 39.90 % Favored : 56.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.29), residues: 913 helix: 2.03 (0.25), residues: 453 sheet: 0.18 (0.61), residues: 70 loop : -0.76 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 152 TYR 0.011 0.002 TYR N 118 PHE 0.013 0.002 PHE M 204 TRP 0.007 0.001 TRP M 169 HIS 0.006 0.001 HIS M 256 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 6583) covalent geometry : angle 0.84274 ( 8978) hydrogen bonds : bond 0.02988 ( 403) hydrogen bonds : angle 4.36269 ( 1176) *********************** 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 152 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 114 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8396 (tm-30) REVERT: G 135 VAL cc_start: 0.8896 (t) cc_final: 0.8525 (m) REVERT: G 150 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.7972 (p0) REVERT: G 174 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8461 (mm-30) REVERT: G 177 GLU cc_start: 0.9114 (tp30) cc_final: 0.8885 (tp30) REVERT: G 187 ASN cc_start: 0.8574 (t0) cc_final: 0.8337 (t0) REVERT: G 193 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7607 (pmm) REVERT: G 197 ARG cc_start: 0.9231 (tpp80) cc_final: 0.8683 (tpp80) REVERT: G 227 GLN cc_start: 0.8997 (tp40) cc_final: 0.8495 (tp-100) REVERT: G 231 ASP cc_start: 0.8290 (m-30) cc_final: 0.7590 (m-30) REVERT: M 64 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8407 (tm-30) REVERT: M 306 TYR cc_start: 0.4556 (OUTLIER) cc_final: 0.2684 (p90) REVERT: N 74 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.7957 (p) REVERT: N 77 GLU cc_start: 0.9136 (mp0) cc_final: 0.8513 (pm20) REVERT: N 79 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8632 (mm) REVERT: N 132 MET cc_start: 0.8748 (mmm) cc_final: 0.8507 (mmm) REVERT: P 55 ASP cc_start: 0.8491 (m-30) cc_final: 0.8133 (p0) REVERT: P 63 LYS cc_start: 0.8335 (tptt) cc_final: 0.7850 (tppt) REVERT: Q 39 PHE cc_start: 0.7366 (m-80) cc_final: 0.6099 (t80) REVERT: Q 41 GLN cc_start: 0.8894 (pp30) cc_final: 0.8315 (tp-100) outliers start: 22 outliers final: 7 residues processed: 143 average time/residue: 0.5874 time to fit residues: 88.0941 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 : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 224 ILE Chi-restraints excluded: chain M residue 306 TYR Chi-restraints excluded: chain N residue 60 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain P residue 60 ILE Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain Q residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 17 optimal weight: 0.0870 chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 45 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 205 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 = 0.3955 r_free = 0.3955 target = 0.096745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.071334 restraints weight = 22217.723| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.82 r_work: 0.3267 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 1.8983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 6583 Z= 0.159 Angle : 0.852 11.961 8978 Z= 0.403 Chirality : 0.046 0.178 1113 Planarity : 0.005 0.052 1192 Dihedral : 4.320 22.415 982 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.76 % Allowed : 41.28 % Favored : 55.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.29), residues: 913 helix: 2.19 (0.25), residues: 445 sheet: 0.21 (0.63), residues: 67 loop : -0.82 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 123 TYR 0.010 0.001 TYR N 118 PHE 0.014 0.002 PHE M 204 TRP 0.005 0.001 TRP M 169 HIS 0.005 0.001 HIS M 256 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 6583) covalent geometry : angle 0.85214 ( 8978) hydrogen bonds : bond 0.02849 ( 403) hydrogen bonds : angle 4.31623 ( 1176) *********************** 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 133 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 123 ARG cc_start: 0.8607 (mmt90) cc_final: 0.8262 (tpp80) REVERT: G 135 VAL cc_start: 0.9030 (t) cc_final: 0.8760 (m) REVERT: G 174 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8521 (mm-30) REVERT: G 193 MET cc_start: 0.7843 (pmt) cc_final: 0.7345 (ppp) REVERT: G 197 ARG cc_start: 0.9113 (tpp80) cc_final: 0.8851 (tpp80) REVERT: G 227 GLN cc_start: 0.8976 (tp40) cc_final: 0.8605 (tp-100) REVERT: G 231 ASP cc_start: 0.8406 (m-30) cc_final: 0.7902 (m-30) REVERT: M 67 MET cc_start: 0.9064 (ttm) cc_final: 0.8446 (mtp) REVERT: M 176 GLU cc_start: 0.7700 (tp30) cc_final: 0.7468 (tp30) REVERT: M 268 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.9030 (pp) REVERT: M 306 TYR cc_start: 0.4651 (OUTLIER) cc_final: 0.2892 (p90) REVERT: N 77 GLU cc_start: 0.9106 (mp0) cc_final: 0.8565 (pm20) REVERT: N 79 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8894 (mm) REVERT: N 92 LEU cc_start: 0.9255 (mp) cc_final: 0.8857 (tt) REVERT: N 95 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.6425 (pm20) REVERT: N 132 MET cc_start: 0.8705 (mmm) cc_final: 0.8461 (mmm) REVERT: Q 39 PHE cc_start: 0.7771 (m-80) cc_final: 0.6106 (t80) REVERT: Q 41 GLN cc_start: 0.8779 (pp30) cc_final: 0.8286 (tp-100) REVERT: Q 73 MET cc_start: 0.7618 (pmm) cc_final: 0.6020 (ptm) REVERT: Q 80 ARG cc_start: 0.7969 (ptp-170) cc_final: 0.7574 (ptp-170) outliers start: 16 outliers final: 10 residues processed: 128 average time/residue: 0.5401 time to fit residues: 72.8345 Evaluate side-chains 118 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 224 ILE Chi-restraints excluded: chain M residue 268 ILE Chi-restraints excluded: chain M residue 306 TYR Chi-restraints excluded: chain N residue 60 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 95 GLU Chi-restraints excluded: chain P residue 60 ILE Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain Q residue 51 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 39 optimal weight: 0.8980 chunk 11 optimal weight: 40.0000 chunk 56 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 1 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 42 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3922 r_free = 0.3922 target = 0.094268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.068562 restraints weight = 22083.904| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 4.01 r_work: 0.3195 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 1.9827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 6583 Z= 0.189 Angle : 0.891 18.749 8978 Z= 0.425 Chirality : 0.048 0.263 1113 Planarity : 0.005 0.050 1192 Dihedral : 4.408 21.947 982 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.29), residues: 913 helix: 2.22 (0.26), residues: 444 sheet: -0.07 (0.63), residues: 70 loop : -0.64 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 121 TYR 0.012 0.002 TYR N 118 PHE 0.014 0.002 PHE M 124 TRP 0.010 0.002 TRP M 169 HIS 0.005 0.001 HIS M 256 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 6583) covalent geometry : angle 0.89089 ( 8978) hydrogen bonds : bond 0.02996 ( 403) hydrogen bonds : angle 4.39584 ( 1176) *********************** 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 129 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 123 ARG cc_start: 0.8595 (mmt90) cc_final: 0.8324 (tpp80) REVERT: G 174 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8361 (mm-30) REVERT: G 193 MET cc_start: 0.8057 (pmt) cc_final: 0.7737 (pmm) REVERT: G 197 ARG cc_start: 0.9150 (tpp80) cc_final: 0.8828 (tpp80) REVERT: G 227 GLN cc_start: 0.9140 (tp40) cc_final: 0.8753 (tp-100) REVERT: G 231 ASP cc_start: 0.8652 (m-30) cc_final: 0.8197 (m-30) REVERT: M 67 MET cc_start: 0.9074 (ttm) cc_final: 0.8568 (mtp) REVERT: M 176 GLU cc_start: 0.7720 (tp30) cc_final: 0.7438 (tp30) REVERT: M 205 HIS cc_start: 0.8068 (t70) cc_final: 0.7692 (t-90) REVERT: M 268 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8837 (pp) REVERT: N 73 MET cc_start: 0.7917 (ppp) cc_final: 0.7693 (tmm) REVERT: N 77 GLU cc_start: 0.9149 (mp0) cc_final: 0.8652 (pm20) REVERT: N 79 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9078 (mm) REVERT: N 121 ARG cc_start: 0.8267 (ttm110) cc_final: 0.8010 (ttm110) REVERT: N 132 MET cc_start: 0.8863 (mmm) cc_final: 0.8644 (mmm) REVERT: P 55 ASP cc_start: 0.9194 (t0) cc_final: 0.8680 (p0) REVERT: P 59 ASP cc_start: 0.8904 (t0) cc_final: 0.8424 (p0) REVERT: P 98 ASP cc_start: 0.7350 (p0) cc_final: 0.7084 (p0) REVERT: Q 39 PHE cc_start: 0.8045 (m-80) cc_final: 0.6215 (t80) REVERT: Q 58 MET cc_start: 0.8043 (ptp) cc_final: 0.7792 (mmm) REVERT: Q 73 MET cc_start: 0.8259 (pmm) cc_final: 0.7324 (ptt) REVERT: Q 80 ARG cc_start: 0.8222 (ptp-170) cc_final: 0.7860 (ptt-90) REVERT: Q 90 ASP cc_start: 0.8363 (p0) cc_final: 0.7932 (m-30) REVERT: Q 95 GLU cc_start: 0.8161 (mp0) cc_final: 0.7913 (mp0) REVERT: Q 130 GLU cc_start: 0.8428 (tt0) cc_final: 0.8083 (tm-30) outliers start: 21 outliers final: 12 residues processed: 121 average time/residue: 0.5999 time to fit residues: 76.2420 Evaluate side-chains 110 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 224 ILE Chi-restraints excluded: chain M residue 268 ILE Chi-restraints excluded: chain N residue 57 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain P residue 60 ILE Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 24 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 chunk 49 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.091702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.065841 restraints weight = 21464.061| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.81 r_work: 0.3151 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 2.0670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 6583 Z= 0.209 Angle : 0.918 15.992 8978 Z= 0.438 Chirality : 0.048 0.197 1113 Planarity : 0.006 0.106 1192 Dihedral : 4.565 21.050 982 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.82 % Favored : 95.07 % Rotamer: Outliers : 3.28 % Allowed : 41.28 % Favored : 55.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.29), residues: 913 helix: 2.24 (0.26), residues: 442 sheet: 0.09 (0.64), residues: 70 loop : -0.67 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG N 121 TYR 0.010 0.001 TYR N 118 PHE 0.018 0.002 PHE M 124 TRP 0.005 0.001 TRP M 169 HIS 0.006 0.001 HIS M 256 Details of bonding type rmsd covalent geometry : bond 0.00503 ( 6583) covalent geometry : angle 0.91800 ( 8978) hydrogen bonds : bond 0.03132 ( 403) hydrogen bonds : angle 4.50485 ( 1176) ********************** 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 123 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 174 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8519 (mm-30) REVERT: G 177 GLU cc_start: 0.9235 (tt0) cc_final: 0.8982 (tm-30) REVERT: G 193 MET cc_start: 0.8150 (pmt) cc_final: 0.7720 (pmm) REVERT: G 197 ARG cc_start: 0.9192 (tpp80) cc_final: 0.8907 (tpp80) REVERT: G 227 GLN cc_start: 0.9119 (tp40) cc_final: 0.8723 (tp-100) REVERT: G 233 MET cc_start: 0.8094 (pmm) cc_final: 0.7765 (pmm) REVERT: M 67 MET cc_start: 0.9060 (ttm) cc_final: 0.8606 (mtp) REVERT: M 176 GLU cc_start: 0.7735 (tp30) cc_final: 0.7465 (tp30) REVERT: N 77 GLU cc_start: 0.9229 (mp0) cc_final: 0.8893 (pm20) REVERT: N 79 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8988 (mm) REVERT: P 53 ASP cc_start: 0.7905 (t70) cc_final: 0.7499 (p0) REVERT: P 55 ASP cc_start: 0.9253 (t0) cc_final: 0.8991 (p0) REVERT: Q 39 PHE cc_start: 0.8146 (m-80) cc_final: 0.6206 (t80) REVERT: Q 58 MET cc_start: 0.8348 (ptp) cc_final: 0.8009 (mmm) REVERT: Q 77 GLU cc_start: 0.7304 (pp20) cc_final: 0.7046 (pm20) REVERT: Q 80 ARG cc_start: 0.8491 (ptp-170) cc_final: 0.8277 (ptp-170) REVERT: Q 90 ASP cc_start: 0.8462 (p0) cc_final: 0.8169 (m-30) REVERT: Q 95 GLU cc_start: 0.8363 (mp0) cc_final: 0.8091 (mp0) REVERT: Q 130 GLU cc_start: 0.8428 (tt0) cc_final: 0.8129 (tm-30) outliers start: 19 outliers final: 10 residues processed: 115 average time/residue: 0.6703 time to fit residues: 80.4820 Evaluate side-chains 102 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 224 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 98 ASP Chi-restraints excluded: chain P residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.0060 chunk 51 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 67 optimal weight: 0.0070 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.4814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.092435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.066890 restraints weight = 21520.535| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.85 r_work: 0.3163 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 2.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6583 Z= 0.166 Angle : 0.894 15.786 8978 Z= 0.425 Chirality : 0.046 0.188 1113 Planarity : 0.006 0.094 1192 Dihedral : 4.449 19.769 982 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.94 % Allowed : 41.80 % Favored : 55.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.29), residues: 913 helix: 2.28 (0.26), residues: 444 sheet: 0.11 (0.65), residues: 67 loop : -0.69 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG M 48 TYR 0.006 0.001 TYR N 118 PHE 0.015 0.001 PHE M 124 TRP 0.010 0.001 TRP M 169 HIS 0.007 0.001 HIS M 256 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 6583) covalent geometry : angle 0.89446 ( 8978) hydrogen bonds : bond 0.02904 ( 403) hydrogen bonds : angle 4.38056 ( 1176) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4040.83 seconds wall clock time: 69 minutes 39.39 seconds (4179.39 seconds total)