Starting phenix.real_space_refine on Thu Mar 13 03:45:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ykv_39373/03_2025/8ykv_39373_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ykv_39373/03_2025/8ykv_39373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ykv_39373/03_2025/8ykv_39373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ykv_39373/03_2025/8ykv_39373.map" model { file = "/net/cci-nas-00/data/ceres_data/8ykv_39373/03_2025/8ykv_39373_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ykv_39373/03_2025/8ykv_39373_neut.cif" } resolution = 2.48 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= 0.099 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: 5 Type Number sf(0) Gaussians S 55 5.16 5 C 5535 2.51 5 N 1466 2.21 5 O 1606 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8665 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1713 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 210} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2578 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1729 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "G" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 443 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2174 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 259} Chain breaks: 3 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'A1LYV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.31, per 1000 atoms: 0.61 Number of scatterers: 8665 At special positions: 0 Unit cell: (86.92, 118.08, 135.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 F 3 9.00 O 1606 8.00 N 1466 7.00 C 5535 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.1 seconds 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2082 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 14 sheets defined 40.8% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.663A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.677A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.446A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.618A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.188A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.083A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.734A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'R' and resid 12 through 45 removed outlier: 3.609A pdb=" N TYR R 25 " --> pdb=" O LEU R 21 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU R 26 " --> pdb=" O GLU R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 74 Processing helix chain 'R' and resid 75 through 86 removed outlier: 4.321A pdb=" N LEU R 79 " --> pdb=" O THR R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 126 Processing helix chain 'R' and resid 131 through 134 Processing helix chain 'R' and resid 135 through 155 Processing helix chain 'R' and resid 156 through 158 No H-bonds generated for 'chain 'R' and resid 156 through 158' Processing helix chain 'R' and resid 174 through 178 Processing helix chain 'R' and resid 180 through 196 Processing helix chain 'R' and resid 196 through 217 Processing helix chain 'R' and resid 227 through 260 removed outlier: 3.536A pdb=" N VAL R 238 " --> pdb=" O VAL R 234 " (cutoff:3.500A) Proline residue: R 247 - end of helix Processing helix chain 'R' and resid 269 through 285 Proline residue: R 282 - end of helix removed outlier: 3.559A pdb=" N PHE R 285 " --> pdb=" O ARG R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 286 through 297 Proline residue: R 292 - end of helix Processing helix chain 'R' and resid 299 through 309 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.730A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.543A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.778A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.754A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.611A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.671A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.430A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.696A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.211A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.211A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.515A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.515A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 479 hydrogen bonds defined for protein. 1308 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: 2.85 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1403 1.29 - 1.43: 2352 1.43 - 1.56: 5004 1.56 - 1.69: 2 1.69 - 1.82: 79 Bond restraints: 8840 Sorted by residual: bond pdb=" C07 A1LYV R 401 " pdb=" N09 A1LYV R 401 " ideal model delta sigma weight residual 1.334 1.448 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C LEU R 79 " pdb=" O LEU R 79 " ideal model delta sigma weight residual 1.236 1.192 0.045 1.26e-02 6.30e+03 1.25e+01 bond pdb=" C07 A1LYV R 401 " pdb=" O08 A1LYV R 401 " ideal model delta sigma weight residual 1.228 1.162 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" CA ASP R 174 " pdb=" C ASP R 174 " ideal model delta sigma weight residual 1.525 1.460 0.065 2.10e-02 2.27e+03 9.62e+00 bond pdb=" C PHE R 175 " pdb=" O PHE R 175 " ideal model delta sigma weight residual 1.236 1.205 0.030 1.18e-02 7.18e+03 6.55e+00 ... (remaining 8835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 11713 1.73 - 3.46: 202 3.46 - 5.18: 49 5.18 - 6.91: 10 6.91 - 8.64: 4 Bond angle restraints: 11978 Sorted by residual: angle pdb=" N PHE R 175 " pdb=" CA PHE R 175 " pdb=" C PHE R 175 " ideal model delta sigma weight residual 111.37 118.40 -7.03 1.65e+00 3.67e-01 1.82e+01 angle pdb=" N MET E 192 " pdb=" CA MET E 192 " pdb=" CB MET E 192 " ideal model delta sigma weight residual 114.17 109.40 4.77 1.14e+00 7.69e-01 1.75e+01 angle pdb=" N ASP A 229 " pdb=" CA ASP A 229 " pdb=" C ASP A 229 " ideal model delta sigma weight residual 112.34 117.14 -4.80 1.30e+00 5.92e-01 1.36e+01 angle pdb=" CA LEU A 232 " pdb=" C LEU A 232 " pdb=" O LEU A 232 " ideal model delta sigma weight residual 121.46 117.49 3.97 1.17e+00 7.31e-01 1.15e+01 angle pdb=" N ALA A 226 " pdb=" CA ALA A 226 " pdb=" C ALA A 226 " ideal model delta sigma weight residual 109.96 105.17 4.79 1.50e+00 4.44e-01 1.02e+01 ... (remaining 11973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 4660 16.90 - 33.81: 392 33.81 - 50.71: 135 50.71 - 67.62: 35 67.62 - 84.52: 12 Dihedral angle restraints: 5234 sinusoidal: 2011 harmonic: 3223 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 158.59 21.41 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA PHE B 151 " pdb=" C PHE B 151 " pdb=" N LEU B 152 " pdb=" CA LEU B 152 " ideal model delta harmonic sigma weight residual 180.00 162.90 17.10 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 163.51 16.49 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 5231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1197 0.060 - 0.120: 155 0.120 - 0.180: 15 0.180 - 0.241: 1 0.241 - 0.301: 1 Chirality restraints: 1369 Sorted by residual: chirality pdb=" CA PHE R 175 " pdb=" N PHE R 175 " pdb=" C PHE R 175 " pdb=" CB PHE R 175 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA LEU A 227 " pdb=" N LEU A 227 " pdb=" C LEU A 227 " pdb=" CB LEU A 227 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA ARG B 304 " pdb=" N ARG B 304 " pdb=" C ARG B 304 " pdb=" CB ARG B 304 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.75e-01 ... (remaining 1366 not shown) Planarity restraints: 1511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 223 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.64e+00 pdb=" C PHE A 223 " -0.033 2.00e-02 2.50e+03 pdb=" O PHE A 223 " 0.012 2.00e-02 2.50e+03 pdb=" N CYS A 224 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 281 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO A 282 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C05 A1LYV R 401 " -0.009 2.00e-02 2.50e+03 1.42e-02 2.53e+00 pdb=" C07 A1LYV R 401 " 0.025 2.00e-02 2.50e+03 pdb=" C10 A1LYV R 401 " 0.005 2.00e-02 2.50e+03 pdb=" N09 A1LYV R 401 " -0.015 2.00e-02 2.50e+03 pdb=" O08 A1LYV R 401 " -0.006 2.00e-02 2.50e+03 ... (remaining 1508 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 56 2.58 - 3.16: 7248 3.16 - 3.74: 13755 3.74 - 4.32: 20012 4.32 - 4.90: 33455 Nonbonded interactions: 74526 Sorted by model distance: nonbonded pdb=" C22 A1LYV R 401 " pdb=" F28 A1LYV R 401 " model vdw 1.997 3.290 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.204 3.040 nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.214 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.313 3.040 nonbonded pdb=" O GLY E 112 " pdb=" OG SER E 184 " model vdw 2.322 3.040 ... (remaining 74521 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: 0.990 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.750 Find NCS groups from input model: 0.100 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:13.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 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 : 0.004 0.114 8840 Z= 0.251 Angle : 0.630 8.638 11978 Z= 0.349 Chirality : 0.042 0.301 1369 Planarity : 0.004 0.049 1511 Dihedral : 15.419 84.523 3152 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.54 % Allowed : 13.87 % Favored : 85.59 % 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: 1.66 (0.26), residues: 1084 helix: 2.48 (0.26), residues: 379 sheet: 0.67 (0.31), residues: 271 loop : 0.22 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.012 0.001 PHE R 115 TYR 0.015 0.001 TYR R 83 ARG 0.006 0.000 ARG R 303 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 142 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: A 208 ARG cc_start: 0.8382 (ttm-80) cc_final: 0.8131 (ttp-110) REVERT: B 197 ARG cc_start: 0.8186 (mmt90) cc_final: 0.7814 (mmm160) REVERT: B 217 MET cc_start: 0.7266 (mmm) cc_final: 0.7017 (mpm) REVERT: R 203 MET cc_start: 0.8086 (ttm) cc_final: 0.7791 (ttt) REVERT: R 296 PHE cc_start: 0.6817 (t80) cc_final: 0.5101 (m-80) outliers start: 5 outliers final: 1 residues processed: 145 average time/residue: 1.4855 time to fit residues: 227.3369 Evaluate side-chains 127 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 294 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 85 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.159735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.105505 restraints weight = 9440.027| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.16 r_work: 0.3114 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8840 Z= 0.173 Angle : 0.542 6.403 11978 Z= 0.292 Chirality : 0.042 0.195 1369 Planarity : 0.004 0.034 1511 Dihedral : 6.637 58.424 1215 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.80 % Allowed : 12.37 % Favored : 84.84 % 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: 1.81 (0.26), residues: 1084 helix: 2.53 (0.26), residues: 387 sheet: 0.90 (0.30), residues: 270 loop : 0.23 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 211 HIS 0.002 0.001 HIS B 91 PHE 0.012 0.001 PHE R 175 TYR 0.010 0.001 TYR A 296 ARG 0.005 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.977 Fit side-chains REVERT: A 208 ARG cc_start: 0.8070 (ttm-80) cc_final: 0.7775 (ttp-110) REVERT: A 306 GLN cc_start: 0.7842 (mm-40) cc_final: 0.7460 (mm110) REVERT: B 130 GLU cc_start: 0.8468 (mp0) cc_final: 0.8261 (mp0) REVERT: B 197 ARG cc_start: 0.8427 (mmt90) cc_final: 0.7777 (mmm160) REVERT: B 215 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: B 217 MET cc_start: 0.7439 (mmm) cc_final: 0.6873 (mmm) REVERT: B 280 LYS cc_start: 0.8780 (tttm) cc_final: 0.8559 (tttp) REVERT: G 15 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7542 (tt) REVERT: R 189 MET cc_start: 0.7772 (tpp) cc_final: 0.7361 (mmt) REVERT: R 215 LYS cc_start: 0.8375 (mttt) cc_final: 0.8171 (mttm) REVERT: R 217 ARG cc_start: 0.7496 (ttm110) cc_final: 0.6996 (ttm-80) REVERT: R 296 PHE cc_start: 0.6574 (t80) cc_final: 0.4840 (m-80) outliers start: 26 outliers final: 7 residues processed: 152 average time/residue: 1.4440 time to fit residues: 232.3964 Evaluate side-chains 132 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain R residue 288 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 30 optimal weight: 3.9990 chunk 66 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 58 optimal weight: 0.3980 chunk 107 optimal weight: 0.0270 chunk 2 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.163452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107541 restraints weight = 9574.463| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.25 r_work: 0.3160 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8840 Z= 0.135 Angle : 0.489 5.837 11978 Z= 0.262 Chirality : 0.041 0.175 1369 Planarity : 0.003 0.032 1511 Dihedral : 6.336 58.331 1214 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.37 % Allowed : 13.87 % Favored : 83.76 % 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: 1.89 (0.26), residues: 1084 helix: 2.72 (0.26), residues: 389 sheet: 0.70 (0.30), residues: 269 loop : 0.32 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.000 HIS A 188 PHE 0.012 0.001 PHE R 63 TYR 0.009 0.001 TYR E 190 ARG 0.004 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.986 Fit side-chains REVERT: A 208 ARG cc_start: 0.7980 (ttm-80) cc_final: 0.7659 (ttp-110) REVERT: A 306 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7462 (mm110) REVERT: B 197 ARG cc_start: 0.8361 (mmt90) cc_final: 0.7714 (mmm160) REVERT: B 217 MET cc_start: 0.7507 (mmm) cc_final: 0.6986 (mmm) REVERT: B 226 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: B 256 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.6390 (mtt180) REVERT: B 280 LYS cc_start: 0.8792 (tttm) cc_final: 0.8585 (tttm) REVERT: E 189 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8324 (mp) REVERT: E 194 ASN cc_start: 0.8795 (m110) cc_final: 0.8498 (m110) REVERT: G 42 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7244 (tp30) REVERT: R 189 MET cc_start: 0.7738 (tpp) cc_final: 0.7288 (mmt) REVERT: R 203 MET cc_start: 0.7917 (ttm) cc_final: 0.7671 (ttt) REVERT: R 217 ARG cc_start: 0.7445 (ttm110) cc_final: 0.6982 (ttm-80) REVERT: R 296 PHE cc_start: 0.6689 (t80) cc_final: 0.4877 (m-80) REVERT: R 307 MET cc_start: 0.3464 (OUTLIER) cc_final: 0.3055 (mpt) outliers start: 22 outliers final: 6 residues processed: 155 average time/residue: 1.3636 time to fit residues: 223.8575 Evaluate side-chains 136 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain R residue 307 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 75 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.160963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.106923 restraints weight = 9663.814| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.17 r_work: 0.3135 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8840 Z= 0.163 Angle : 0.505 6.644 11978 Z= 0.268 Chirality : 0.041 0.187 1369 Planarity : 0.003 0.040 1511 Dihedral : 6.240 58.270 1214 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.58 % Allowed : 15.59 % Favored : 81.83 % 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: 1.87 (0.26), residues: 1084 helix: 2.75 (0.26), residues: 389 sheet: 0.54 (0.30), residues: 279 loop : 0.38 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 188 PHE 0.014 0.001 PHE R 63 TYR 0.011 0.001 TYR R 100 ARG 0.005 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.993 Fit side-chains REVERT: A 208 ARG cc_start: 0.7964 (ttm-80) cc_final: 0.7681 (ttp-110) REVERT: A 306 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7449 (mm110) REVERT: B 197 ARG cc_start: 0.8391 (mmt90) cc_final: 0.7725 (mmm160) REVERT: B 215 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: B 217 MET cc_start: 0.7411 (mmm) cc_final: 0.6966 (mmm) REVERT: B 256 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6399 (mtt180) REVERT: B 280 LYS cc_start: 0.8791 (tttm) cc_final: 0.8581 (tttm) REVERT: E 189 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8349 (mp) REVERT: G 38 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7819 (ttp) REVERT: G 42 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6981 (mt-10) REVERT: R 189 MET cc_start: 0.7751 (tpp) cc_final: 0.7397 (mmt) REVERT: R 217 ARG cc_start: 0.7427 (ttm110) cc_final: 0.6824 (tpp-160) REVERT: R 296 PHE cc_start: 0.6692 (t80) cc_final: 0.4887 (m-80) REVERT: R 307 MET cc_start: 0.3497 (OUTLIER) cc_final: 0.3062 (mpt) outliers start: 24 outliers final: 9 residues processed: 138 average time/residue: 1.4489 time to fit residues: 210.9674 Evaluate side-chains 134 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 307 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 0.0470 chunk 101 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.158311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.103989 restraints weight = 9475.729| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.14 r_work: 0.3093 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8840 Z= 0.221 Angle : 0.528 7.385 11978 Z= 0.281 Chirality : 0.042 0.145 1369 Planarity : 0.004 0.037 1511 Dihedral : 6.308 59.854 1214 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.33 % Allowed : 15.38 % Favored : 81.29 % 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: 1.83 (0.26), residues: 1084 helix: 2.67 (0.26), residues: 389 sheet: 0.52 (0.30), residues: 292 loop : 0.38 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.006 0.001 HIS A 188 PHE 0.014 0.002 PHE R 63 TYR 0.013 0.001 TYR E 103 ARG 0.005 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 1.053 Fit side-chains REVERT: A 208 ARG cc_start: 0.7971 (ttm-80) cc_final: 0.7674 (ttp-110) REVERT: B 197 ARG cc_start: 0.8416 (mmt90) cc_final: 0.7744 (mmm160) REVERT: B 215 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: B 217 MET cc_start: 0.7407 (mmm) cc_final: 0.6895 (mmm) REVERT: B 256 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.6478 (mtt180) REVERT: E 163 LYS cc_start: 0.8286 (mtpp) cc_final: 0.7961 (tttt) REVERT: E 189 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8423 (mp) REVERT: G 38 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7849 (ttp) REVERT: G 42 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7032 (mt-10) REVERT: R 189 MET cc_start: 0.7724 (tpp) cc_final: 0.7355 (mmt) REVERT: R 203 MET cc_start: 0.7960 (ttm) cc_final: 0.7744 (ttt) REVERT: R 217 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.6952 (tpt90) REVERT: R 296 PHE cc_start: 0.6711 (t80) cc_final: 0.4841 (m-80) REVERT: R 307 MET cc_start: 0.3498 (OUTLIER) cc_final: 0.3030 (mpt) outliers start: 31 outliers final: 12 residues processed: 142 average time/residue: 1.5066 time to fit residues: 226.7311 Evaluate side-chains 139 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 217 ARG Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 307 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 106 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.158423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.104243 restraints weight = 9419.023| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.13 r_work: 0.3098 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8840 Z= 0.205 Angle : 0.519 6.455 11978 Z= 0.277 Chirality : 0.042 0.200 1369 Planarity : 0.004 0.041 1511 Dihedral : 6.208 57.369 1214 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.30 % Allowed : 14.95 % Favored : 80.75 % 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: 1.76 (0.26), residues: 1084 helix: 2.65 (0.26), residues: 389 sheet: 0.48 (0.30), residues: 292 loop : 0.31 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS A 188 PHE 0.033 0.002 PHE R 63 TYR 0.012 0.001 TYR E 103 ARG 0.004 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 1.282 Fit side-chains REVERT: A 208 ARG cc_start: 0.7965 (ttm-80) cc_final: 0.7632 (ttp-110) REVERT: B 197 ARG cc_start: 0.8386 (mmt90) cc_final: 0.7695 (mmm160) REVERT: B 215 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: B 217 MET cc_start: 0.7427 (mmm) cc_final: 0.6955 (mmm) REVERT: B 256 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.6494 (mtt180) REVERT: E 163 LYS cc_start: 0.8234 (mtpp) cc_final: 0.7781 (tttt) REVERT: E 189 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8383 (mp) REVERT: G 38 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7795 (ttp) REVERT: G 42 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7066 (mt-10) REVERT: R 189 MET cc_start: 0.7736 (tpp) cc_final: 0.7349 (mmt) REVERT: R 203 MET cc_start: 0.7950 (ttm) cc_final: 0.7680 (ttt) REVERT: R 217 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.6877 (tpt90) REVERT: R 296 PHE cc_start: 0.6722 (t80) cc_final: 0.4846 (m-80) REVERT: R 307 MET cc_start: 0.3552 (OUTLIER) cc_final: 0.2978 (mpt) outliers start: 40 outliers final: 18 residues processed: 150 average time/residue: 1.3626 time to fit residues: 216.8779 Evaluate side-chains 143 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 217 ARG Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 288 SER Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 307 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.158964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.104800 restraints weight = 9520.608| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.15 r_work: 0.3106 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8840 Z= 0.181 Angle : 0.511 7.241 11978 Z= 0.271 Chirality : 0.041 0.176 1369 Planarity : 0.004 0.039 1511 Dihedral : 6.070 55.657 1214 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.55 % Allowed : 15.70 % Favored : 80.75 % 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: 1.74 (0.26), residues: 1084 helix: 2.76 (0.26), residues: 387 sheet: 0.40 (0.30), residues: 277 loop : 0.23 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS A 188 PHE 0.010 0.001 PHE R 115 TYR 0.011 0.001 TYR E 103 ARG 0.004 0.000 ARG R 281 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.990 Fit side-chains REVERT: A 22 ASN cc_start: 0.8369 (m110) cc_final: 0.8010 (m110) REVERT: A 208 ARG cc_start: 0.7932 (ttm-80) cc_final: 0.7617 (ttp-110) REVERT: B 197 ARG cc_start: 0.8380 (mmt90) cc_final: 0.7688 (mmm160) REVERT: B 215 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: B 217 MET cc_start: 0.7485 (mmm) cc_final: 0.6984 (mmm) REVERT: B 256 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.6502 (mtt180) REVERT: E 43 LYS cc_start: 0.7956 (mtpm) cc_final: 0.7383 (mttp) REVERT: E 163 LYS cc_start: 0.8211 (mtpp) cc_final: 0.7842 (tttt) REVERT: E 189 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8314 (mp) REVERT: G 38 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7663 (ttp) REVERT: G 42 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.6949 (mm-30) REVERT: R 189 MET cc_start: 0.7709 (tpp) cc_final: 0.7350 (mmt) REVERT: R 203 MET cc_start: 0.7927 (ttm) cc_final: 0.7611 (ttt) REVERT: R 217 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6880 (tpt90) REVERT: R 296 PHE cc_start: 0.6741 (t80) cc_final: 0.4891 (m-80) REVERT: R 307 MET cc_start: 0.3427 (OUTLIER) cc_final: 0.2904 (mpt) outliers start: 33 outliers final: 15 residues processed: 143 average time/residue: 1.4569 time to fit residues: 219.8004 Evaluate side-chains 147 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 217 ARG Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 307 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 64 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.155591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.098425 restraints weight = 9480.817| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.22 r_work: 0.3026 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 8840 Z= 0.413 Angle : 0.642 8.351 11978 Z= 0.338 Chirality : 0.047 0.217 1369 Planarity : 0.004 0.040 1511 Dihedral : 6.636 56.867 1214 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.87 % Allowed : 16.56 % Favored : 79.57 % 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: 1.39 (0.26), residues: 1084 helix: 2.36 (0.26), residues: 389 sheet: 0.36 (0.30), residues: 270 loop : 0.02 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.008 0.001 HIS A 188 PHE 0.036 0.002 PHE R 63 TYR 0.020 0.002 TYR E 103 ARG 0.006 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 1.015 Fit side-chains REVERT: A 22 ASN cc_start: 0.8435 (m110) cc_final: 0.8047 (m110) REVERT: A 208 ARG cc_start: 0.8003 (ttm-80) cc_final: 0.7674 (ttp-110) REVERT: B 197 ARG cc_start: 0.8455 (mmt90) cc_final: 0.7720 (mmm160) REVERT: B 215 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: B 217 MET cc_start: 0.7473 (mmm) cc_final: 0.6980 (mmm) REVERT: B 256 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.6583 (mtp180) REVERT: E 3 GLN cc_start: 0.8575 (tt0) cc_final: 0.8339 (tt0) REVERT: E 43 LYS cc_start: 0.8048 (mtpm) cc_final: 0.7427 (mttp) REVERT: E 163 LYS cc_start: 0.8277 (mtpp) cc_final: 0.7798 (tttt) REVERT: G 38 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7947 (ttp) REVERT: G 42 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7132 (mt-10) REVERT: R 203 MET cc_start: 0.7998 (ttm) cc_final: 0.7710 (ttt) REVERT: R 217 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6991 (tpt90) REVERT: R 296 PHE cc_start: 0.6857 (t80) cc_final: 0.4902 (m-80) REVERT: R 297 LEU cc_start: 0.7371 (mp) cc_final: 0.6924 (mp) REVERT: R 307 MET cc_start: 0.3403 (OUTLIER) cc_final: 0.2871 (mpt) outliers start: 36 outliers final: 15 residues processed: 149 average time/residue: 1.4613 time to fit residues: 229.5653 Evaluate side-chains 143 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain R residue 217 ARG Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 288 SER Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 307 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 15 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.156559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.099995 restraints weight = 9417.928| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.20 r_work: 0.3050 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8840 Z= 0.293 Angle : 0.582 8.751 11978 Z= 0.307 Chirality : 0.044 0.178 1369 Planarity : 0.004 0.039 1511 Dihedral : 6.533 56.013 1214 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.01 % Allowed : 17.20 % Favored : 79.78 % 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: 1.37 (0.26), residues: 1084 helix: 2.41 (0.26), residues: 387 sheet: 0.26 (0.30), residues: 276 loop : 0.04 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.007 0.001 HIS A 188 PHE 0.014 0.002 PHE R 115 TYR 0.016 0.002 TYR E 103 ARG 0.007 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8418 (m110) cc_final: 0.8040 (m110) REVERT: A 208 ARG cc_start: 0.8004 (ttm-80) cc_final: 0.7678 (ttp-110) REVERT: B 197 ARG cc_start: 0.8437 (mmt90) cc_final: 0.7726 (mmm160) REVERT: B 215 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: B 217 MET cc_start: 0.7416 (mmm) cc_final: 0.6898 (mmm) REVERT: B 226 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8440 (mt-10) REVERT: B 256 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.6546 (mtt180) REVERT: E 3 GLN cc_start: 0.8571 (tt0) cc_final: 0.8329 (tt0) REVERT: E 163 LYS cc_start: 0.8282 (mtpp) cc_final: 0.7881 (tttt) REVERT: E 189 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8338 (mp) REVERT: G 38 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7799 (ttp) REVERT: G 42 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7060 (mt-10) REVERT: R 63 PHE cc_start: 0.7034 (t80) cc_final: 0.6828 (t80) REVERT: R 189 MET cc_start: 0.7783 (tpp) cc_final: 0.7444 (mmt) REVERT: R 203 MET cc_start: 0.7997 (ttm) cc_final: 0.7711 (ttt) REVERT: R 217 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.6907 (tpt90) REVERT: R 296 PHE cc_start: 0.6870 (t80) cc_final: 0.4958 (m-80) REVERT: R 297 LEU cc_start: 0.7397 (mp) cc_final: 0.6957 (mp) REVERT: R 307 MET cc_start: 0.3389 (OUTLIER) cc_final: 0.2838 (mpt) outliers start: 28 outliers final: 15 residues processed: 145 average time/residue: 1.5065 time to fit residues: 229.9751 Evaluate side-chains 145 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain R residue 217 ARG Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 307 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 63 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.158488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.102249 restraints weight = 9411.459| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.20 r_work: 0.3086 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8840 Z= 0.200 Angle : 0.537 9.232 11978 Z= 0.283 Chirality : 0.042 0.150 1369 Planarity : 0.004 0.038 1511 Dihedral : 6.268 56.578 1214 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.58 % Allowed : 17.53 % Favored : 79.89 % 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: 1.49 (0.26), residues: 1084 helix: 2.50 (0.26), residues: 388 sheet: 0.29 (0.30), residues: 281 loop : 0.12 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS A 188 PHE 0.012 0.001 PHE R 285 TYR 0.012 0.001 TYR E 103 ARG 0.008 0.000 ARG E 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 1.494 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8390 (m110) cc_final: 0.8029 (m110) REVERT: A 208 ARG cc_start: 0.7975 (ttm-80) cc_final: 0.7665 (ttp-110) REVERT: B 197 ARG cc_start: 0.8418 (mmt90) cc_final: 0.7701 (mmm160) REVERT: B 215 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: B 217 MET cc_start: 0.7427 (mmm) cc_final: 0.6961 (mmm) REVERT: B 226 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8420 (mt-10) REVERT: B 256 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.6500 (mtt180) REVERT: E 3 GLN cc_start: 0.8540 (tt0) cc_final: 0.8293 (tt0) REVERT: E 43 LYS cc_start: 0.7923 (mtpm) cc_final: 0.7312 (mttp) REVERT: E 163 LYS cc_start: 0.8249 (mtpp) cc_final: 0.7812 (tttt) REVERT: E 189 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8250 (mp) REVERT: G 38 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7770 (ttp) REVERT: G 42 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7049 (mt-10) REVERT: R 63 PHE cc_start: 0.7032 (t80) cc_final: 0.6821 (t80) REVERT: R 189 MET cc_start: 0.7815 (tpp) cc_final: 0.7488 (mmt) REVERT: R 203 MET cc_start: 0.7956 (ttm) cc_final: 0.7657 (ttt) REVERT: R 217 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.6917 (tpt90) REVERT: R 296 PHE cc_start: 0.6831 (t80) cc_final: 0.4921 (m-80) REVERT: R 307 MET cc_start: 0.3392 (OUTLIER) cc_final: 0.2803 (mpt) outliers start: 24 outliers final: 15 residues processed: 144 average time/residue: 1.6744 time to fit residues: 254.5199 Evaluate side-chains 149 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 217 ARG Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 307 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 103 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.157718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.103816 restraints weight = 9547.805| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.13 r_work: 0.3091 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8840 Z= 0.199 Angle : 0.534 9.078 11978 Z= 0.281 Chirality : 0.042 0.150 1369 Planarity : 0.004 0.036 1511 Dihedral : 6.120 54.511 1214 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.90 % Allowed : 16.77 % Favored : 80.32 % 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: 1.51 (0.26), residues: 1084 helix: 2.56 (0.26), residues: 388 sheet: 0.29 (0.30), residues: 276 loop : 0.09 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS A 188 PHE 0.011 0.001 PHE R 115 TYR 0.012 0.001 TYR E 103 ARG 0.008 0.000 ARG E 160 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 9208.72 seconds wall clock time: 158 minutes 5.78 seconds (9485.78 seconds total)