Starting phenix.real_space_refine on Thu Feb 13 07:43:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x9a_33069/02_2025/7x9a_33069.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x9a_33069/02_2025/7x9a_33069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x9a_33069/02_2025/7x9a_33069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x9a_33069/02_2025/7x9a_33069.map" model { file = "/net/cci-nas-00/data/ceres_data/7x9a_33069/02_2025/7x9a_33069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x9a_33069/02_2025/7x9a_33069.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2000 atoms to isotropic. 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 54 5.16 5 C 4591 2.51 5 N 1210 2.21 5 O 1301 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7156 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2427 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "A" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1623 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 62 Chain: "B" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2443 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 115 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 103 Chain: "C" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 384 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "P" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 279 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 31} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 4.61, per 1000 atoms: 0.64 Number of scatterers: 7156 At special positions: 0 Unit cell: (114.95, 124.355, 85.69, 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 54 16.00 O 1301 8.00 N 1210 7.00 C 4591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 33 " - pdb=" SG CYS R 296 " distance=2.03 Simple disulfide: pdb=" SG CYS R 113 " - pdb=" SG CYS R 198 " distance=2.03 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: 1.84 Conformation dependent library (CDL) restraints added in 1.1 seconds 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1810 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 9 sheets defined 43.4% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'R' and resid 37 through 67 removed outlier: 3.686A pdb=" N PHE R 41 " --> pdb=" O LEU R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 104 removed outlier: 3.978A pdb=" N ILE R 77 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU R 94 " --> pdb=" O ALA R 90 " (cutoff:3.500A) Proline residue: R 95 - end of helix removed outlier: 3.675A pdb=" N LEU R 102 " --> pdb=" O PHE R 98 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP R 104 " --> pdb=" O TYR R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 143 Proline residue: R 117 - end of helix Processing helix chain 'R' and resid 151 through 171 Processing helix chain 'R' and resid 171 through 176 Processing helix chain 'R' and resid 204 through 220 Processing helix chain 'R' and resid 221 through 245 removed outlier: 3.694A pdb=" N ILE R 234 " --> pdb=" O CYS R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 287 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 297 through 320 removed outlier: 4.141A pdb=" N LEU R 303 " --> pdb=" O ASN R 299 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA R 309 " --> pdb=" O CYS R 305 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N CYS R 314 " --> pdb=" O MET R 310 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN R 316 " --> pdb=" O SER R 312 " (cutoff:3.500A) Proline residue: R 317 - end of helix Processing helix chain 'R' and resid 324 through 329 removed outlier: 3.608A pdb=" N ARG R 329 " --> pdb=" O LYS R 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 33 Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.640A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 50' Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.699A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.798A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 11 through 25 removed outlier: 3.599A pdb=" N LYS B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 22 removed outlier: 4.033A pdb=" N GLU C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'P' and resid 13 through 32 Processing sheet with id=AA1, first strand: chain 'R' and resid 178 through 180 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 7.081A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS A 322 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.450A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.301A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.673A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.507A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.452A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.418A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 278 358 hydrogen bonds defined for protein. 1035 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: 2.03 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2312 1.34 - 1.46: 1772 1.46 - 1.58: 3151 1.58 - 1.70: 0 1.70 - 1.82: 75 Bond restraints: 7310 Sorted by residual: bond pdb=" CB TYC P 36 " pdb=" CG TYC P 36 " ideal model delta sigma weight residual 1.501 1.391 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" N TRP R 288 " pdb=" CA TRP R 288 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.22e-02 6.72e+03 6.25e+00 bond pdb=" C LEU R 277 " pdb=" N PRO R 278 " ideal model delta sigma weight residual 1.334 1.361 -0.028 2.34e-02 1.83e+03 1.39e+00 bond pdb=" C ASP R 287 " pdb=" N TRP R 288 " ideal model delta sigma weight residual 1.332 1.344 -0.012 1.29e-02 6.01e+03 8.44e-01 bond pdb=" C LEU R 218 " pdb=" N GLN R 219 " ideal model delta sigma weight residual 1.334 1.347 -0.013 1.52e-02 4.33e+03 7.38e-01 ... (remaining 7305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 9866 1.87 - 3.74: 77 3.74 - 5.61: 18 5.61 - 7.48: 4 7.48 - 9.35: 1 Bond angle restraints: 9966 Sorted by residual: angle pdb=" CA LEU R 94 " pdb=" CB LEU R 94 " pdb=" CG LEU R 94 " ideal model delta sigma weight residual 116.30 125.65 -9.35 3.50e+00 8.16e-02 7.14e+00 angle pdb=" C TRP R 288 " pdb=" N ASN R 289 " pdb=" CA ASN R 289 " ideal model delta sigma weight residual 121.54 126.18 -4.64 1.91e+00 2.74e-01 5.89e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 121.54 126.15 -4.61 1.91e+00 2.74e-01 5.83e+00 angle pdb=" CA TRP R 288 " pdb=" C TRP R 288 " pdb=" O TRP R 288 " ideal model delta sigma weight residual 119.59 116.74 2.85 1.18e+00 7.18e-01 5.82e+00 angle pdb=" CA TRP R 288 " pdb=" CB TRP R 288 " pdb=" CG TRP R 288 " ideal model delta sigma weight residual 113.60 109.22 4.38 1.90e+00 2.77e-01 5.32e+00 ... (remaining 9961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.37: 3997 15.37 - 30.74: 230 30.74 - 46.11: 57 46.11 - 61.48: 5 61.48 - 76.85: 2 Dihedral angle restraints: 4291 sinusoidal: 1507 harmonic: 2784 Sorted by residual: dihedral pdb=" CB CYS R 33 " pdb=" SG CYS R 33 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual -86.00 -116.46 30.46 1 1.00e+01 1.00e-02 1.32e+01 dihedral pdb=" CA ASP R 86 " pdb=" CB ASP R 86 " pdb=" CG ASP R 86 " pdb=" OD1 ASP R 86 " ideal model delta sinusoidal sigma weight residual -30.00 -85.72 55.72 1 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CA ASP R 31 " pdb=" CB ASP R 31 " pdb=" CG ASP R 31 " pdb=" OD1 ASP R 31 " ideal model delta sinusoidal sigma weight residual -30.00 -80.64 50.64 1 2.00e+01 2.50e-03 8.78e+00 ... (remaining 4288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 764 0.033 - 0.066: 309 0.066 - 0.099: 79 0.099 - 0.131: 24 0.131 - 0.164: 2 Chirality restraints: 1178 Sorted by residual: chirality pdb=" CA TRP R 288 " pdb=" N TRP R 288 " pdb=" C TRP R 288 " pdb=" CB TRP R 288 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.74e-01 chirality pdb=" CA LEU R 94 " pdb=" N LEU R 94 " pdb=" C LEU R 94 " pdb=" CB LEU R 94 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 1175 not shown) Planarity restraints: 1262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 288 " -0.012 2.00e-02 2.50e+03 8.43e-03 1.77e+00 pdb=" CG TRP R 288 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP R 288 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP R 288 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 288 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP R 288 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP R 288 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 288 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 288 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP R 288 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 171 " -0.021 5.00e-02 4.00e+02 3.14e-02 1.57e+00 pdb=" N PRO R 172 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO R 172 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 172 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 222 " -0.020 5.00e-02 4.00e+02 3.05e-02 1.48e+00 pdb=" N PRO R 223 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO R 223 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 223 " -0.017 5.00e-02 4.00e+02 ... (remaining 1259 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1639 2.78 - 3.31: 7039 3.31 - 3.84: 12063 3.84 - 4.37: 13598 4.37 - 4.90: 23507 Nonbonded interactions: 57846 Sorted by model distance: nonbonded pdb=" O TRP R 276 " pdb=" OG1 THR R 280 " model vdw 2.251 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.257 3.040 nonbonded pdb=" O LEU B 210 " pdb=" N ARG B 219 " model vdw 2.284 3.120 nonbonded pdb=" ND2 ASN B 119 " pdb=" O GLY B 144 " model vdw 2.293 3.120 nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.339 3.040 ... (remaining 57841 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.300 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 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 : 0.002 0.110 7310 Z= 0.121 Angle : 0.489 9.352 9966 Z= 0.262 Chirality : 0.039 0.164 1178 Planarity : 0.003 0.031 1262 Dihedral : 10.375 76.846 2475 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.79 (0.25), residues: 935 helix: -0.73 (0.24), residues: 392 sheet: -1.88 (0.36), residues: 172 loop : -3.01 (0.27), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 288 HIS 0.002 0.000 HIS B 142 PHE 0.006 0.001 PHE B 241 TYR 0.013 0.001 TYR R 100 ARG 0.001 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.779 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: A 287 TYR cc_start: 0.8313 (m-10) cc_final: 0.7954 (m-80) REVERT: B 138 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7730 (mt-10) REVERT: B 264 TYR cc_start: 0.7707 (m-10) cc_final: 0.7114 (m-10) REVERT: B 297 TRP cc_start: 0.7084 (m100) cc_final: 0.6548 (m100) REVERT: C 47 GLU cc_start: 0.7950 (mp0) cc_final: 0.7697 (mp0) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2124 time to fit residues: 61.1414 Evaluate side-chains 149 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 GLN R 326 ASN A 244 HIS A 347 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.105412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.086562 restraints weight = 19438.997| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.96 r_work: 0.3335 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7310 Z= 0.191 Angle : 0.591 9.944 9966 Z= 0.295 Chirality : 0.042 0.167 1178 Planarity : 0.003 0.038 1262 Dihedral : 3.560 29.001 1017 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.03 % Allowed : 14.72 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.78 (0.27), residues: 935 helix: 0.22 (0.27), residues: 403 sheet: -1.74 (0.35), residues: 178 loop : -2.50 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.007 0.001 HIS P 26 PHE 0.024 0.001 PHE B 199 TYR 0.012 0.001 TYR C 40 ARG 0.004 0.000 ARG R 260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 120 GLN cc_start: 0.8684 (mt0) cc_final: 0.8423 (mt0) REVERT: R 153 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.7230 (mmt180) REVERT: R 248 MET cc_start: 0.6619 (ptp) cc_final: 0.6339 (ptp) REVERT: A 18 MET cc_start: 0.8914 (ppp) cc_final: 0.8252 (ppp) REVERT: A 216 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7710 (mm-30) REVERT: A 258 TRP cc_start: 0.8686 (m100) cc_final: 0.7866 (m100) REVERT: B 138 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8468 (mt-10) REVERT: B 156 GLN cc_start: 0.7906 (mt0) cc_final: 0.7570 (mt0) REVERT: B 211 TRP cc_start: 0.7725 (OUTLIER) cc_final: 0.6727 (m100) REVERT: B 297 TRP cc_start: 0.8323 (m100) cc_final: 0.7595 (m100) outliers start: 22 outliers final: 15 residues processed: 181 average time/residue: 0.1831 time to fit residues: 45.1120 Evaluate side-chains 169 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 153 ARG Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 298 HIS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 83 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 28 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 326 ASN A 213 HIS A 269 ASN A 322 HIS ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.102156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.083138 restraints weight = 19549.149| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.94 r_work: 0.3265 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7310 Z= 0.203 Angle : 0.591 9.666 9966 Z= 0.293 Chirality : 0.041 0.173 1178 Planarity : 0.003 0.040 1262 Dihedral : 3.669 30.409 1017 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.44 % Allowed : 16.64 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.32 (0.28), residues: 935 helix: 0.61 (0.27), residues: 404 sheet: -1.68 (0.35), residues: 177 loop : -2.14 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS B 225 PHE 0.019 0.001 PHE A 250 TYR 0.016 0.001 TYR A 287 ARG 0.004 0.000 ARG R 260 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 200 ASP cc_start: 0.7799 (p0) cc_final: 0.7572 (p0) REVERT: R 248 MET cc_start: 0.6758 (ptp) cc_final: 0.6412 (ptp) REVERT: A 187 THR cc_start: 0.8806 (OUTLIER) cc_final: 0.8539 (p) REVERT: A 274 PHE cc_start: 0.8530 (t80) cc_final: 0.8326 (t80) REVERT: B 211 TRP cc_start: 0.7825 (OUTLIER) cc_final: 0.6882 (m100) REVERT: B 264 TYR cc_start: 0.8250 (m-10) cc_final: 0.7850 (m-10) REVERT: B 292 PHE cc_start: 0.7967 (m-10) cc_final: 0.7641 (m-10) REVERT: B 297 TRP cc_start: 0.8290 (m100) cc_final: 0.7653 (m100) REVERT: C 21 MET cc_start: 0.7596 (tmm) cc_final: 0.7393 (tmm) outliers start: 25 outliers final: 19 residues processed: 173 average time/residue: 0.1756 time to fit residues: 41.3038 Evaluate side-chains 168 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 298 HIS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 65 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN R 76 ASN ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.101978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.082823 restraints weight = 19792.958| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.99 r_work: 0.3258 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7310 Z= 0.182 Angle : 0.576 9.830 9966 Z= 0.285 Chirality : 0.041 0.195 1178 Planarity : 0.003 0.041 1262 Dihedral : 3.628 29.040 1017 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.44 % Allowed : 18.43 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.05 (0.28), residues: 935 helix: 0.74 (0.28), residues: 407 sheet: -1.42 (0.37), residues: 157 loop : -1.99 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.017 0.001 PHE B 199 TYR 0.023 0.001 TYR A 287 ARG 0.005 0.000 ARG R 260 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 52 ILE cc_start: 0.9334 (pt) cc_final: 0.9084 (tp) REVERT: R 76 ASN cc_start: 0.9299 (m110) cc_final: 0.8964 (m110) REVERT: R 93 CYS cc_start: 0.8932 (m) cc_final: 0.8325 (m) REVERT: R 153 ARG cc_start: 0.7685 (mmt180) cc_final: 0.7435 (mmp-170) REVERT: R 248 MET cc_start: 0.6916 (ptp) cc_final: 0.6644 (ptp) REVERT: A 18 MET cc_start: 0.8898 (ppp) cc_final: 0.8217 (ppp) REVERT: A 258 TRP cc_start: 0.8800 (m100) cc_final: 0.8564 (m100) REVERT: A 286 CYS cc_start: 0.8524 (t) cc_final: 0.8188 (t) REVERT: A 287 TYR cc_start: 0.7066 (m-80) cc_final: 0.6756 (m-10) REVERT: B 264 TYR cc_start: 0.8143 (m-10) cc_final: 0.7716 (m-10) REVERT: B 292 PHE cc_start: 0.8112 (m-10) cc_final: 0.7549 (m-10) REVERT: B 297 TRP cc_start: 0.8278 (m100) cc_final: 0.7613 (m100) REVERT: C 21 MET cc_start: 0.7635 (tmm) cc_final: 0.7367 (tmm) outliers start: 25 outliers final: 19 residues processed: 179 average time/residue: 0.1883 time to fit residues: 46.5527 Evaluate side-chains 163 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 CYS Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain P residue 31 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 35 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 14 optimal weight: 0.3980 chunk 42 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.101273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.082212 restraints weight = 19641.963| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.90 r_work: 0.3238 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7310 Z= 0.190 Angle : 0.580 9.903 9966 Z= 0.288 Chirality : 0.041 0.195 1178 Planarity : 0.003 0.041 1262 Dihedral : 3.673 29.258 1017 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.26 % Allowed : 18.29 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.78 (0.28), residues: 935 helix: 0.96 (0.28), residues: 400 sheet: -1.40 (0.38), residues: 146 loop : -1.72 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.016 0.001 PHE A 250 TYR 0.015 0.001 TYR A 287 ARG 0.006 0.000 ARG R 260 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 52 ILE cc_start: 0.9336 (pt) cc_final: 0.9086 (tp) REVERT: R 93 CYS cc_start: 0.8954 (m) cc_final: 0.8346 (m) REVERT: R 153 ARG cc_start: 0.7750 (mmt180) cc_final: 0.7493 (mmp-170) REVERT: R 248 MET cc_start: 0.6975 (ptp) cc_final: 0.6700 (ptp) REVERT: A 216 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8020 (mm-30) REVERT: A 258 TRP cc_start: 0.8797 (m100) cc_final: 0.8537 (m100) REVERT: A 274 PHE cc_start: 0.8396 (t80) cc_final: 0.8190 (t80) REVERT: B 45 MET cc_start: 0.8559 (ttp) cc_final: 0.8298 (mtp) REVERT: B 292 PHE cc_start: 0.8268 (m-10) cc_final: 0.7801 (m-10) REVERT: B 297 TRP cc_start: 0.8285 (m100) cc_final: 0.7630 (m100) outliers start: 31 outliers final: 28 residues processed: 172 average time/residue: 0.1685 time to fit residues: 39.8330 Evaluate side-chains 174 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 CYS Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 225 CYS Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 298 HIS Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain P residue 31 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 85 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 0.0570 chunk 68 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 86 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.101116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.082632 restraints weight = 19484.905| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.83 r_work: 0.3245 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7310 Z= 0.181 Angle : 0.587 9.868 9966 Z= 0.290 Chirality : 0.041 0.215 1178 Planarity : 0.003 0.041 1262 Dihedral : 3.697 29.576 1017 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.13 % Allowed : 18.84 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.61 (0.29), residues: 935 helix: 1.07 (0.28), residues: 400 sheet: -1.30 (0.37), residues: 162 loop : -1.59 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.016 0.001 PHE A 250 TYR 0.008 0.001 TYR R 47 ARG 0.006 0.000 ARG R 260 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 39 MET cc_start: 0.8304 (ptp) cc_final: 0.8051 (ptp) REVERT: R 52 ILE cc_start: 0.9358 (pt) cc_final: 0.9104 (tp) REVERT: R 153 ARG cc_start: 0.7729 (mmt180) cc_final: 0.7511 (mmp-170) REVERT: R 248 MET cc_start: 0.6909 (ptp) cc_final: 0.6507 (ptp) REVERT: A 18 MET cc_start: 0.8809 (ppp) cc_final: 0.8161 (ppp) REVERT: A 274 PHE cc_start: 0.8440 (t80) cc_final: 0.8230 (t80) REVERT: A 287 TYR cc_start: 0.7058 (m-80) cc_final: 0.6704 (m-10) REVERT: B 57 LYS cc_start: 0.8878 (ptpp) cc_final: 0.8528 (ptpt) REVERT: B 262 MET cc_start: 0.6844 (ttt) cc_final: 0.6616 (ttt) REVERT: B 264 TYR cc_start: 0.8145 (m-10) cc_final: 0.6872 (m-10) REVERT: B 292 PHE cc_start: 0.8297 (m-10) cc_final: 0.7605 (m-10) REVERT: B 297 TRP cc_start: 0.8258 (m100) cc_final: 0.7578 (m100) outliers start: 30 outliers final: 27 residues processed: 168 average time/residue: 0.1818 time to fit residues: 42.0763 Evaluate side-chains 169 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 CYS Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 298 HIS Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 84 optimal weight: 0.0270 chunk 88 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.5240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.101361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.082309 restraints weight = 19377.242| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.94 r_work: 0.3250 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7310 Z= 0.169 Angle : 0.596 9.916 9966 Z= 0.293 Chirality : 0.041 0.209 1178 Planarity : 0.003 0.042 1262 Dihedral : 3.713 29.689 1017 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.40 % Allowed : 19.26 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.57 (0.28), residues: 935 helix: 1.08 (0.28), residues: 400 sheet: -1.32 (0.37), residues: 166 loop : -1.52 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.016 0.001 PHE A 250 TYR 0.007 0.001 TYR R 47 ARG 0.007 0.000 ARG R 260 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 39 MET cc_start: 0.8311 (ptp) cc_final: 0.7940 (ptm) REVERT: R 43 LEU cc_start: 0.8875 (mp) cc_final: 0.8673 (mp) REVERT: R 52 ILE cc_start: 0.9363 (pt) cc_final: 0.9120 (tp) REVERT: R 248 MET cc_start: 0.7005 (ptp) cc_final: 0.6651 (ptp) REVERT: A 18 MET cc_start: 0.8830 (ppp) cc_final: 0.8167 (ppp) REVERT: B 57 LYS cc_start: 0.8912 (ptpp) cc_final: 0.8578 (ptpt) REVERT: B 264 TYR cc_start: 0.8150 (m-10) cc_final: 0.6953 (m-10) REVERT: B 292 PHE cc_start: 0.8373 (m-10) cc_final: 0.7655 (m-10) REVERT: B 297 TRP cc_start: 0.8271 (m100) cc_final: 0.7552 (m100) outliers start: 32 outliers final: 27 residues processed: 172 average time/residue: 0.1749 time to fit residues: 41.3517 Evaluate side-chains 162 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 CYS Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 298 HIS Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 GLN A 294 ASN A 306 GLN B 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.099624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.080464 restraints weight = 19492.058| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.92 r_work: 0.3211 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7310 Z= 0.224 Angle : 0.625 9.626 9966 Z= 0.311 Chirality : 0.042 0.217 1178 Planarity : 0.003 0.040 1262 Dihedral : 3.848 28.527 1017 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.54 % Allowed : 20.50 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.56 (0.29), residues: 935 helix: 1.09 (0.28), residues: 400 sheet: -1.46 (0.35), residues: 170 loop : -1.42 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.003 0.001 HIS B 225 PHE 0.014 0.001 PHE A 250 TYR 0.010 0.001 TYR B 59 ARG 0.008 0.000 ARG R 260 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 52 ILE cc_start: 0.9401 (pt) cc_final: 0.9142 (tp) REVERT: R 92 MET cc_start: 0.8133 (tpt) cc_final: 0.7776 (tpt) REVERT: R 248 MET cc_start: 0.6998 (ptp) cc_final: 0.6647 (ptp) REVERT: B 57 LYS cc_start: 0.8887 (ptpp) cc_final: 0.8435 (ptpt) REVERT: B 292 PHE cc_start: 0.8616 (m-10) cc_final: 0.7838 (m-10) REVERT: B 297 TRP cc_start: 0.8280 (m100) cc_final: 0.7583 (m100) outliers start: 33 outliers final: 28 residues processed: 158 average time/residue: 0.1757 time to fit residues: 38.1739 Evaluate side-chains 165 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 CYS Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 298 HIS Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 54 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 0.0570 chunk 34 optimal weight: 0.0870 chunk 87 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.101412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.082904 restraints weight = 19502.782| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.88 r_work: 0.3251 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7310 Z= 0.180 Angle : 0.639 10.937 9966 Z= 0.315 Chirality : 0.041 0.212 1178 Planarity : 0.003 0.040 1262 Dihedral : 3.858 29.584 1017 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.58 % Allowed : 21.87 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.65 (0.28), residues: 935 helix: 1.03 (0.28), residues: 406 sheet: -1.38 (0.36), residues: 170 loop : -1.60 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.030 0.001 PHE A 274 TYR 0.007 0.001 TYR B 59 ARG 0.008 0.000 ARG R 260 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 52 ILE cc_start: 0.9391 (pt) cc_final: 0.9134 (tp) REVERT: R 248 MET cc_start: 0.6919 (ptp) cc_final: 0.6563 (ptp) REVERT: A 18 MET cc_start: 0.8895 (ppp) cc_final: 0.8200 (ppp) REVERT: B 57 LYS cc_start: 0.8921 (ptpp) cc_final: 0.8638 (ptpt) REVERT: B 264 TYR cc_start: 0.8115 (m-10) cc_final: 0.6928 (m-10) REVERT: B 292 PHE cc_start: 0.8554 (m-10) cc_final: 0.7790 (m-10) REVERT: B 297 TRP cc_start: 0.8229 (m100) cc_final: 0.7457 (m100) outliers start: 26 outliers final: 22 residues processed: 164 average time/residue: 0.1713 time to fit residues: 39.4064 Evaluate side-chains 158 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 CYS Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 298 HIS Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 37 optimal weight: 0.0270 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.101334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.082746 restraints weight = 20026.318| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.94 r_work: 0.3240 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7310 Z= 0.190 Angle : 0.656 10.646 9966 Z= 0.319 Chirality : 0.042 0.225 1178 Planarity : 0.003 0.041 1262 Dihedral : 3.826 27.569 1017 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.85 % Allowed : 22.01 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.28), residues: 935 helix: 0.99 (0.28), residues: 406 sheet: -1.35 (0.37), residues: 163 loop : -1.52 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.014 0.001 PHE A 250 TYR 0.008 0.001 TYR B 59 ARG 0.009 0.000 ARG R 260 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 52 ILE cc_start: 0.9404 (pt) cc_final: 0.9154 (tp) REVERT: R 248 MET cc_start: 0.6863 (ptp) cc_final: 0.6412 (ptp) REVERT: A 18 MET cc_start: 0.8890 (ppp) cc_final: 0.8193 (ppp) REVERT: A 298 GLU cc_start: 0.9361 (tt0) cc_final: 0.8982 (tt0) REVERT: B 264 TYR cc_start: 0.8145 (m-10) cc_final: 0.6940 (m-10) REVERT: B 292 PHE cc_start: 0.8579 (m-10) cc_final: 0.7822 (m-10) REVERT: B 297 TRP cc_start: 0.8260 (m100) cc_final: 0.7504 (m100) outliers start: 28 outliers final: 26 residues processed: 162 average time/residue: 0.1669 time to fit residues: 37.7931 Evaluate side-chains 167 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 CYS Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 132 VAL Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 298 HIS Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 76 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 89 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.100835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.082414 restraints weight = 19414.186| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 3.84 r_work: 0.3234 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7310 Z= 0.208 Angle : 0.667 10.864 9966 Z= 0.327 Chirality : 0.042 0.216 1178 Planarity : 0.003 0.041 1262 Dihedral : 3.870 26.817 1017 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.85 % Allowed : 22.56 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.70 (0.28), residues: 935 helix: 0.91 (0.27), residues: 407 sheet: -1.19 (0.39), residues: 148 loop : -1.67 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.021 0.001 PHE A 274 TYR 0.007 0.001 TYR R 220 ARG 0.009 0.000 ARG R 260 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3770.58 seconds wall clock time: 67 minutes 38.14 seconds (4058.14 seconds total)