Starting phenix.real_space_refine on Sat May 10 15:53:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n49_48871/05_2025/9n49_48871.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n49_48871/05_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_48871/05_2025/9n49_48871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n49_48871/05_2025/9n49_48871.map" model { file = "/net/cci-nas-00/data/ceres_data/9n49_48871/05_2025/9n49_48871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n49_48871/05_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-5687/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: 12.19, per 1000 atoms: 1.87 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: 1.67 Conformation dependent library (CDL) restraints added in 1.5 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: 0.83 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: 2.22 Time building geometry restraints manager: 1.96 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: 36.640 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 28.210 Find NCS groups from input model: 0.220 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: 0.010 Load rotamer database and sin/cos tables:12.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.240 ------------------------------------------------------------------------------- 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 : 0.647 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: 1.1840 time to fit residues: 239.0714 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 : 0.711 ------------------------------------------------------------------------------- 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 = 63)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.082008 restraints weight = 20277.882| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.43 r_work: 0.3448 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3704 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 : 0.736 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: 0.6889 (mt) cc_final: 0.6586 (mp) REVERT: G 150 ASP cc_start: 0.6408 (OUTLIER) cc_final: 0.6160 (p0) REVERT: G 174 GLU cc_start: 0.6568 (tp30) cc_final: 0.5907 (tm-30) REVERT: G 177 GLU cc_start: 0.6293 (tp30) cc_final: 0.5531 (tm-30) REVERT: G 188 LEU cc_start: 0.7963 (pt) cc_final: 0.7301 (tt) REVERT: G 227 GLN cc_start: 0.8608 (tp40) cc_final: 0.8346 (tp40) REVERT: M 224 ILE cc_start: 0.5638 (OUTLIER) cc_final: 0.4827 (mt) REVERT: N 77 GLU cc_start: 0.7610 (pm20) cc_final: 0.7322 (pm20) REVERT: P 77 GLU cc_start: 0.4490 (OUTLIER) cc_final: 0.4215 (mt-10) REVERT: P 114 VAL cc_start: 0.5531 (OUTLIER) cc_final: 0.5223 (t) REVERT: P 116 ASP cc_start: 0.6354 (t0) cc_final: 0.6139 (t0) REVERT: Q 118 TYR cc_start: 0.5719 (m-10) cc_final: 0.5079 (m-10) outliers start: 34 outliers final: 6 residues processed: 156 average time/residue: 0.8419 time to fit residues: 139.8815 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 : 0.643 ------------------------------------------------------------------------------- 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: 0.0370 chunk 84 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 89 optimal weight: 0.5980 chunk 54 optimal weight: 0.3980 chunk 36 optimal weight: 0.0060 chunk 12 optimal weight: 30.0000 chunk 33 optimal weight: 6.9990 chunk 71 optimal weight: 0.0000 chunk 45 optimal weight: 0.8980 overall best weight: 0.1878 ------------------------------------------------------------------------------- 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 ** 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 = 0.4063 r_free = 0.4063 target = 0.106393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.084259 restraints weight = 20940.479| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.50 r_work: 0.3512 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4035 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6583 Z= 0.145 Angle : 0.689 9.354 8978 Z= 0.333 Chirality : 0.044 0.150 1113 Planarity : 0.005 0.075 1192 Dihedral : 3.884 26.784 984 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.84 % Allowed : 27.12 % 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: 1.23 (0.29), residues: 913 helix: 2.10 (0.25), residues: 452 sheet: 0.24 (0.54), residues: 85 loop : -0.65 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 169 HIS 0.007 0.001 HIS G 126 PHE 0.025 0.002 PHE G 149 TYR 0.007 0.001 TYR P 104 ARG 0.009 0.001 ARG Q 80 Details of bonding type rmsd hydrogen bonds : bond 0.03148 ( 403) hydrogen bonds : angle 4.51898 ( 1176) covalent geometry : bond 0.00311 ( 6583) covalent geometry : angle 0.68901 ( 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 145 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 146 LEU cc_start: 0.5686 (tt) cc_final: 0.5169 (tp) REVERT: G 150 ASP cc_start: 0.6935 (OUTLIER) cc_final: 0.6722 (p0) REVERT: G 174 GLU cc_start: 0.6831 (tp30) cc_final: 0.5888 (tt0) REVERT: G 177 GLU cc_start: 0.6472 (tp30) cc_final: 0.5663 (tm-30) REVERT: G 188 LEU cc_start: 0.7886 (pt) cc_final: 0.7107 (tt) REVERT: G 193 MET cc_start: 0.2715 (mpp) cc_final: 0.2047 (tpp) REVERT: M 184 MET cc_start: 0.1740 (pmm) cc_final: -0.0783 (tpp) REVERT: M 249 ASN cc_start: 0.5590 (m-40) cc_final: 0.5214 (p0) REVERT: M 306 TYR cc_start: 0.3189 (OUTLIER) cc_final: 0.1392 (p90) REVERT: N 77 GLU cc_start: 0.7625 (pm20) cc_final: 0.7213 (pm20) REVERT: P 102 ASN cc_start: 0.5161 (t0) cc_final: 0.4677 (t0) REVERT: Q 73 MET cc_start: 0.2497 (pmm) cc_final: 0.2152 (pmm) REVERT: Q 75 ILE cc_start: 0.1006 (OUTLIER) cc_final: 0.0749 (mm) REVERT: Q 118 TYR cc_start: 0.5839 (m-10) cc_final: 0.5390 (m-10) outliers start: 28 outliers final: 6 residues processed: 138 average time/residue: 1.0113 time to fit residues: 148.7816 Evaluate side-chains 107 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 112 VAL Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain Q residue 75 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 70 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 20 optimal weight: 0.0470 chunk 41 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 M 312 GLN Q 108 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.109595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.089587 restraints weight = 22750.483| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 3.69 r_work: 0.3652 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5596 moved from start: 0.9277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.145 6583 Z= 0.255 Angle : 0.883 11.104 8978 Z= 0.440 Chirality : 0.051 0.339 1113 Planarity : 0.006 0.071 1192 Dihedral : 4.291 17.208 982 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 6.91 % Allowed : 27.81 % Favored : 65.28 % 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: 0.82 (0.28), residues: 913 helix: 1.92 (0.25), residues: 442 sheet: 0.55 (0.56), residues: 81 loop : -1.12 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP M 246 HIS 0.012 0.002 HIS M 148 PHE 0.022 0.003 PHE M 61 TYR 0.036 0.002 TYR Q 104 ARG 0.013 0.001 ARG N 121 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 403) hydrogen bonds : angle 5.01686 ( 1176) covalent geometry : bond 0.00563 ( 6583) covalent geometry : angle 0.88337 ( 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 214 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 113 MET cc_start: 0.5031 (tmt) cc_final: 0.4121 (ppp) REVERT: G 158 MET cc_start: 0.7479 (mmp) cc_final: 0.7185 (mmt) REVERT: G 177 GLU cc_start: 0.7561 (tp30) cc_final: 0.7112 (tt0) REVERT: M 184 MET cc_start: 0.6020 (pmm) cc_final: 0.5438 (mtp) REVERT: M 249 ASN cc_start: 0.6337 (m-40) cc_final: 0.5652 (p0) REVERT: M 306 TYR cc_start: 0.3810 (OUTLIER) cc_final: 0.2139 (p90) REVERT: N 54 ILE cc_start: 0.6249 (mt) cc_final: 0.5914 (mm) REVERT: N 76 LYS cc_start: 0.6002 (mptt) cc_final: 0.5703 (mptt) REVERT: N 80 ARG cc_start: 0.4949 (OUTLIER) cc_final: 0.4695 (mmp-170) REVERT: Q 101 ILE cc_start: 0.4299 (OUTLIER) cc_final: 0.4066 (tt) outliers start: 40 outliers final: 10 residues processed: 198 average time/residue: 0.9368 time to fit residues: 196.5845 Evaluate side-chains 137 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 155 ASN Chi-restraints excluded: chain M residue 306 TYR Chi-restraints excluded: chain N residue 80 ARG Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 118 TYR Chi-restraints excluded: chain P residue 121 ARG Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 101 ILE Chi-restraints excluded: chain Q residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 31 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 49 optimal weight: 2.9990 chunk 36 optimal weight: 0.0770 chunk 3 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 20.0000 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 116 GLN ** M 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 95 ASN M 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.109879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.089251 restraints weight = 23427.186| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 3.78 r_work: 0.3656 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 1.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 6583 Z= 0.230 Angle : 0.911 15.272 8978 Z= 0.438 Chirality : 0.052 0.295 1113 Planarity : 0.006 0.061 1192 Dihedral : 4.305 15.856 982 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 6.39 % Allowed : 31.95 % Favored : 61.66 % 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: 0.77 (0.28), residues: 913 helix: 1.76 (0.25), residues: 451 sheet: 0.30 (0.59), residues: 65 loop : -0.93 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP M 169 HIS 0.022 0.004 HIS M 148 PHE 0.017 0.003 PHE M 92 TYR 0.027 0.003 TYR N 118 ARG 0.019 0.001 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 403) hydrogen bonds : angle 4.72737 ( 1176) covalent geometry : bond 0.00502 ( 6583) covalent geometry : angle 0.91114 ( 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 202 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 121 LEU cc_start: 0.5673 (tp) cc_final: 0.5313 (tp) REVERT: G 150 ASP cc_start: 0.7749 (t70) cc_final: 0.7469 (p0) REVERT: G 188 LEU cc_start: 0.8203 (pt) cc_final: 0.7979 (pt) REVERT: G 227 GLN cc_start: 0.8618 (tp40) cc_final: 0.8211 (tp40) REVERT: M 146 PHE cc_start: 0.7618 (m-80) cc_final: 0.7413 (m-10) REVERT: M 306 TYR cc_start: 0.3879 (OUTLIER) cc_final: 0.2166 (p90) REVERT: M 321 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8136 (pp) REVERT: N 54 ILE cc_start: 0.6486 (mt) cc_final: 0.6186 (mm) REVERT: N 73 MET cc_start: 0.5348 (ppp) cc_final: 0.4606 (ppp) REVERT: N 95 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6613 (pm20) REVERT: N 110 GLU cc_start: 0.6902 (tp30) cc_final: 0.6694 (tp30) REVERT: P 77 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8301 (mp0) outliers start: 37 outliers final: 6 residues processed: 186 average time/residue: 0.9886 time to fit residues: 194.2377 Evaluate side-chains 133 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 306 TYR Chi-restraints excluded: chain M residue 321 ILE Chi-restraints excluded: chain N residue 95 GLU Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 44 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 28 optimal weight: 8.9990 chunk 84 optimal weight: 0.0070 chunk 51 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 310 ASN P 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.107205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.083766 restraints weight = 22464.046| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 3.93 r_work: 0.3543 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 1.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6583 Z= 0.175 Angle : 0.839 10.088 8978 Z= 0.410 Chirality : 0.048 0.234 1113 Planarity : 0.005 0.057 1192 Dihedral : 4.018 22.305 982 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % 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 (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: 1.04 (0.28), residues: 913 helix: 2.02 (0.25), residues: 453 sheet: 0.38 (0.60), residues: 68 loop : -0.88 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 169 HIS 0.006 0.001 HIS G 126 PHE 0.024 0.002 PHE G 149 TYR 0.018 0.002 TYR N 104 ARG 0.013 0.001 ARG N 121 Details of bonding type rmsd hydrogen bonds : bond 0.03179 ( 403) hydrogen bonds : angle 4.38568 ( 1176) covalent geometry : bond 0.00407 ( 6583) covalent geometry : angle 0.83865 ( 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 167 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 116 GLN cc_start: 0.6917 (pm20) cc_final: 0.6504 (pm20) REVERT: G 120 ASP cc_start: 0.7150 (m-30) cc_final: 0.6736 (m-30) REVERT: G 135 VAL cc_start: 0.8699 (t) cc_final: 0.8446 (m) REVERT: G 152 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7433 (tmm-80) REVERT: G 177 GLU cc_start: 0.8904 (tp30) cc_final: 0.8357 (tt0) REVERT: G 227 GLN cc_start: 0.8714 (tp40) cc_final: 0.8161 (tp40) REVERT: M 67 MET cc_start: 0.8437 (tmm) cc_final: 0.8203 (tmm) REVERT: M 216 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8620 (p0) REVERT: M 306 TYR cc_start: 0.3956 (OUTLIER) cc_final: 0.2047 (p90) REVERT: N 54 ILE cc_start: 0.6798 (mt) cc_final: 0.6493 (mm) REVERT: N 73 MET cc_start: 0.5429 (ppp) cc_final: 0.5052 (ppp) REVERT: N 79 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7792 (mm) REVERT: N 92 LEU cc_start: 0.8961 (mm) cc_final: 0.8599 (tm) REVERT: P 77 GLU cc_start: 0.8955 (mp0) cc_final: 0.8580 (mp0) REVERT: P 134 ARG cc_start: 0.7468 (mmm160) cc_final: 0.7006 (mmm160) outliers start: 26 outliers final: 7 residues processed: 158 average time/residue: 0.9514 time to fit residues: 159.3016 Evaluate side-chains 130 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 152 ARG Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 84 ILE Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain M residue 216 ASN Chi-restraints excluded: chain M residue 306 TYR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 118 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 85 optimal weight: 0.0970 chunk 69 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 81 optimal weight: 0.0470 chunk 68 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.4876 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.104784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.079830 restraints weight = 22744.535| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.94 r_work: 0.3452 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 1.6049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6583 Z= 0.177 Angle : 0.852 12.073 8978 Z= 0.413 Chirality : 0.047 0.229 1113 Planarity : 0.005 0.058 1192 Dihedral : 4.207 27.916 982 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.97 % Allowed : 39.72 % 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 (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: 452 sheet: 0.77 (0.62), residues: 58 loop : -0.78 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 169 HIS 0.003 0.001 HIS M 256 PHE 0.015 0.002 PHE G 149 TYR 0.014 0.002 TYR P 104 ARG 0.011 0.001 ARG M 94 Details of bonding type rmsd hydrogen bonds : bond 0.03057 ( 403) hydrogen bonds : angle 4.29135 ( 1176) covalent geometry : bond 0.00423 ( 6583) covalent geometry : angle 0.85201 ( 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 167 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 116 GLN cc_start: 0.7633 (pm20) cc_final: 0.7353 (tm-30) REVERT: G 124 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8247 (p0) REVERT: G 135 VAL cc_start: 0.8773 (t) cc_final: 0.8407 (m) REVERT: G 150 ASP cc_start: 0.7955 (t70) cc_final: 0.7414 (p0) REVERT: G 152 ARG cc_start: 0.8444 (ppt170) cc_final: 0.8163 (ppp80) REVERT: G 193 MET cc_start: 0.7252 (mmp) cc_final: 0.6638 (pmm) REVERT: G 227 GLN cc_start: 0.8861 (tp40) cc_final: 0.8224 (tp40) REVERT: G 231 ASP cc_start: 0.7963 (m-30) cc_final: 0.7505 (m-30) REVERT: M 67 MET cc_start: 0.8662 (tmm) cc_final: 0.8209 (tmm) REVERT: M 301 VAL cc_start: 0.9474 (t) cc_final: 0.9269 (m) REVERT: M 306 TYR cc_start: 0.4372 (OUTLIER) cc_final: 0.2478 (p90) REVERT: N 54 ILE cc_start: 0.7295 (mt) cc_final: 0.6923 (mm) REVERT: N 79 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8251 (mm) REVERT: N 110 GLU cc_start: 0.7156 (tp30) cc_final: 0.6949 (tp30) REVERT: P 58 MET cc_start: 0.5753 (mpt) cc_final: 0.5258 (mpp) REVERT: P 64 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7453 (tm) REVERT: P 118 TYR cc_start: 0.5826 (OUTLIER) cc_final: 0.3645 (t80) REVERT: Q 95 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8029 (pm20) REVERT: Q 132 MET cc_start: 0.8463 (mmt) cc_final: 0.8163 (mmp) outliers start: 23 outliers final: 8 residues processed: 158 average time/residue: 1.0685 time to fit residues: 177.6710 Evaluate side-chains 124 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 154 ARG Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain M residue 306 TYR 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 64 LEU Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 118 TYR Chi-restraints excluded: chain Q residue 65 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 51 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 141 GLN ** M 87 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 = 0.3999 r_free = 0.3999 target = 0.098668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.073305 restraints weight = 22029.619| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.97 r_work: 0.3313 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 1.8386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 6583 Z= 0.217 Angle : 0.952 11.867 8978 Z= 0.465 Chirality : 0.050 0.211 1113 Planarity : 0.006 0.065 1192 Dihedral : 4.556 21.721 982 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.45 % Allowed : 42.31 % Favored : 54.23 % 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: 1.08 (0.29), residues: 913 helix: 2.08 (0.26), residues: 446 sheet: 0.19 (0.62), residues: 58 loop : -0.77 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 169 HIS 0.005 0.001 HIS M 256 PHE 0.024 0.003 PHE M 61 TYR 0.010 0.002 TYR N 104 ARG 0.016 0.001 ARG P 70 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 403) hydrogen bonds : angle 4.52318 ( 1176) covalent geometry : bond 0.00542 ( 6583) covalent geometry : angle 0.95213 ( 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 147 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 150 ASP cc_start: 0.8429 (t70) cc_final: 0.7878 (p0) REVERT: G 152 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8346 (ppp80) REVERT: G 177 GLU cc_start: 0.9335 (tp30) cc_final: 0.8951 (tt0) REVERT: G 193 MET cc_start: 0.7908 (mmp) cc_final: 0.7361 (ppp) REVERT: G 197 ARG cc_start: 0.9208 (tpp80) cc_final: 0.8979 (tpp80) REVERT: G 227 GLN cc_start: 0.8915 (tp40) cc_final: 0.8490 (tp40) REVERT: G 231 ASP cc_start: 0.8066 (m-30) cc_final: 0.7731 (m-30) REVERT: M 159 LYS cc_start: 0.9268 (mtpp) cc_final: 0.9007 (tttm) REVERT: M 216 ASN cc_start: 0.9056 (OUTLIER) cc_final: 0.8071 (p0) REVERT: M 306 TYR cc_start: 0.4707 (OUTLIER) cc_final: 0.2864 (p90) REVERT: N 74 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7637 (t) REVERT: N 77 GLU cc_start: 0.9158 (mp0) cc_final: 0.8584 (pm20) REVERT: N 79 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8606 (mm) REVERT: N 97 LEU cc_start: 0.6077 (mt) cc_final: 0.5768 (mp) REVERT: N 132 MET cc_start: 0.8322 (mmm) cc_final: 0.8088 (mmm) REVERT: P 58 MET cc_start: 0.6073 (mpt) cc_final: 0.5852 (mpt) REVERT: P 67 GLU cc_start: 0.7278 (tm-30) cc_final: 0.7059 (tm-30) REVERT: P 72 ARG cc_start: 0.8889 (tpp80) cc_final: 0.8618 (mtp85) REVERT: P 77 GLU cc_start: 0.9050 (mp0) cc_final: 0.8691 (mp0) REVERT: P 118 TYR cc_start: 0.7571 (OUTLIER) cc_final: 0.5524 (t80) REVERT: Q 41 GLN cc_start: 0.8847 (pp30) cc_final: 0.8592 (tp-100) REVERT: Q 73 MET cc_start: 0.7658 (pmm) cc_final: 0.6586 (ptm) REVERT: Q 90 ASP cc_start: 0.8225 (p0) cc_final: 0.7746 (m-30) REVERT: Q 95 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8311 (pm20) REVERT: Q 132 MET cc_start: 0.9054 (mmt) cc_final: 0.8775 (mmp) outliers start: 20 outliers final: 3 residues processed: 140 average time/residue: 1.1084 time to fit residues: 163.2112 Evaluate side-chains 111 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 152 ARG Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain M residue 216 ASN Chi-restraints excluded: chain M residue 306 TYR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 118 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.3659 > 50: distance: 16 - 136: 30.753 distance: 19 - 133: 27.789 distance: 88 - 92: 24.274 distance: 92 - 93: 23.979 distance: 93 - 94: 34.369 distance: 93 - 96: 20.058 distance: 94 - 95: 42.479 distance: 94 - 100: 21.480 distance: 96 - 97: 35.690 distance: 97 - 98: 7.273 distance: 97 - 99: 38.516 distance: 100 - 101: 31.878 distance: 101 - 102: 21.631 distance: 101 - 104: 34.112 distance: 102 - 103: 45.229 distance: 102 - 107: 18.182 distance: 104 - 105: 25.647 distance: 104 - 106: 26.227 distance: 107 - 108: 16.136 distance: 108 - 109: 31.331 distance: 108 - 111: 26.951 distance: 109 - 110: 8.715 distance: 109 - 116: 38.265 distance: 111 - 112: 41.693 distance: 112 - 113: 24.654 distance: 113 - 115: 16.067 distance: 116 - 117: 39.590 distance: 117 - 118: 11.725 distance: 118 - 119: 34.131 distance: 118 - 120: 39.098 distance: 120 - 121: 5.484 distance: 121 - 122: 24.963 distance: 121 - 124: 40.033 distance: 122 - 123: 17.646 distance: 122 - 126: 23.791 distance: 124 - 125: 33.578 distance: 126 - 127: 30.246 distance: 127 - 128: 32.777 distance: 127 - 130: 15.028 distance: 128 - 129: 11.719 distance: 128 - 133: 11.557 distance: 130 - 131: 21.922 distance: 130 - 132: 45.664 distance: 133 - 134: 24.672 distance: 134 - 135: 44.393 distance: 134 - 137: 39.788 distance: 135 - 136: 25.744 distance: 135 - 140: 17.828 distance: 137 - 138: 25.053 distance: 137 - 139: 26.638 distance: 140 - 141: 19.443 distance: 141 - 142: 28.479 distance: 141 - 144: 38.184 distance: 142 - 143: 33.576 distance: 142 - 145: 21.457 distance: 145 - 146: 10.037 distance: 146 - 149: 23.765 distance: 147 - 148: 25.761 distance: 147 - 153: 20.306 distance: 149 - 150: 14.941 distance: 150 - 151: 3.543 distance: 150 - 152: 15.630 distance: 153 - 154: 15.142 distance: 154 - 155: 13.913 distance: 154 - 157: 17.350 distance: 155 - 156: 9.786 distance: 155 - 161: 26.284 distance: 157 - 158: 10.856 distance: 158 - 159: 37.368 distance: 158 - 160: 8.014