Starting phenix.real_space_refine on Fri Sep 11 06:15:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rmg_24569/09_2026/7rmg_24569.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rmg_24569/09_2026/7rmg_24569.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rmg_24569/09_2026/7rmg_24569.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rmg_24569/09_2026/7rmg_24569.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7rmg_24569/09_2026/7rmg_24569.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rmg_24569/09_2026/7rmg_24569.cif" model { file = "/net/cci-nas-00/data/ceres_data/7rmg_24569/09_2026/7rmg_24569.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rmg_24569/09_2026/7rmg_24569.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.412 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 1082 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 53 5.16 5 C 4737 2.51 5 N 1226 2.21 5 O 1300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7316 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1510 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 2, 'ARG:plan': 7, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 71 Chain: "R" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2306 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 14, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'PHE:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 43 Chain: "S" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 84 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 8} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2319 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 5, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 7, 'ASP:plan': 13, 'ASN:plan1': 5, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 113 Chain: "G" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 245 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "N" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 851 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 1.77, per 1000 atoms: 0.24 Number of scatterers: 7316 At special positions: 0 Unit cell: (70.14, 96.86, 131.93, 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 53 16.00 O 1300 8.00 N 1226 7.00 C 4737 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 180 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 412.5 milliseconds 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1838 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 11 sheets defined 39.4% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 25 through 38 removed outlier: 3.515A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP A 33 " --> pdb=" O GLN A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.626A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 312 through 316 removed outlier: 4.080A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 350 removed outlier: 3.587A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.553A pdb=" N ARG A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 60 removed outlier: 3.988A pdb=" N ILE R 42 " --> pdb=" O ALA R 38 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS R 60 " --> pdb=" O ILE R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 96 removed outlier: 4.352A pdb=" N HIS R 95 " --> pdb=" O THR R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 136 removed outlier: 4.233A pdb=" N TYR R 104 " --> pdb=" O TYR R 100 " (cutoff:3.500A) Proline residue: R 112 - end of helix Processing helix chain 'R' and resid 143 through 168 Proline residue: R 164 - end of helix Processing helix chain 'R' and resid 190 through 225 removed outlier: 5.024A pdb=" N LEU R 207 " --> pdb=" O LEU R 203 " (cutoff:3.500A) Proline residue: R 208 - end of helix removed outlier: 3.586A pdb=" N ALA R 225 " --> pdb=" O ILE R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 239 through 270 removed outlier: 3.646A pdb=" N LYS R 243 " --> pdb=" O GLN R 239 " (cutoff:3.500A) Proline residue: R 263 - end of helix Processing helix chain 'R' and resid 271 through 273 No H-bonds generated for 'chain 'R' and resid 271 through 273' Processing helix chain 'R' and resid 274 through 280 removed outlier: 3.907A pdb=" N LEU R 277 " --> pdb=" O ASN R 274 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR R 278 " --> pdb=" O PRO R 275 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU R 279 " --> pdb=" O ASP R 276 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS R 280 " --> pdb=" O LEU R 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 274 through 280' Processing helix chain 'R' and resid 281 through 296 Processing helix chain 'R' and resid 299 through 309 removed outlier: 3.915A pdb=" N ILE R 303 " --> pdb=" O MET R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 309 through 320 Processing helix chain 'B' and resid 15 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 14 through 24 removed outlier: 3.832A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.577A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.768A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.389A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 169 through 174 Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.988A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.652A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.600A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.719A 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: 3.993A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.759A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.953A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.596A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 58 through 60 removed outlier: 5.165A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) 383 hydrogen bonds defined for protein. 1098 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1362 1.33 - 1.45: 2058 1.45 - 1.58: 3997 1.58 - 1.71: 0 1.71 - 1.83: 75 Bond restraints: 7492 Sorted by residual: bond pdb=" C ILE A 382 " pdb=" O ILE A 382 " ideal model delta sigma weight residual 1.237 1.202 0.035 1.19e-02 7.06e+03 8.43e+00 bond pdb=" N ILE B 58 " pdb=" CA ILE B 58 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.24e-02 6.50e+03 7.66e+00 bond pdb=" C ASP A 381 " pdb=" O ASP A 381 " ideal model delta sigma weight residual 1.236 1.202 0.034 1.26e-02 6.30e+03 7.24e+00 bond pdb=" N ILE A 382 " pdb=" CA ILE A 382 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.21e-02 6.83e+03 7.09e+00 bond pdb=" C ILE B 58 " pdb=" O ILE B 58 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.20e-02 6.94e+03 6.84e+00 ... (remaining 7487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 9839 1.73 - 3.46: 313 3.46 - 5.20: 55 5.20 - 6.93: 11 6.93 - 8.66: 8 Bond angle restraints: 10226 Sorted by residual: angle pdb=" CA ILE A 382 " pdb=" C ILE A 382 " pdb=" O ILE A 382 " ideal model delta sigma weight residual 120.85 116.82 4.03 1.06e+00 8.90e-01 1.45e+01 angle pdb=" O ILE A 382 " pdb=" C ILE A 382 " pdb=" N ILE A 383 " ideal model delta sigma weight residual 121.83 125.41 -3.58 1.03e+00 9.43e-01 1.21e+01 angle pdb=" O LYS A 380 " pdb=" C LYS A 380 " pdb=" N ASP A 381 " ideal model delta sigma weight residual 122.12 118.52 3.60 1.06e+00 8.90e-01 1.15e+01 angle pdb=" N PHE R 111 " pdb=" CA PHE R 111 " pdb=" C PHE R 111 " ideal model delta sigma weight residual 109.81 117.17 -7.36 2.21e+00 2.05e-01 1.11e+01 angle pdb=" CA LYS A 380 " pdb=" C LYS A 380 " pdb=" N ASP A 381 " ideal model delta sigma weight residual 117.30 121.10 -3.80 1.16e+00 7.43e-01 1.08e+01 ... (remaining 10221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.21: 3968 16.21 - 32.41: 294 32.41 - 48.61: 50 48.61 - 64.82: 11 64.82 - 81.02: 9 Dihedral angle restraints: 4332 sinusoidal: 1495 harmonic: 2837 Sorted by residual: dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -154.28 -25.72 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -156.50 -23.50 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA TYR R 205 " pdb=" C TYR R 205 " pdb=" N PHE R 206 " pdb=" CA PHE R 206 " ideal model delta harmonic sigma weight residual 180.00 -160.45 -19.55 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 4329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 786 0.041 - 0.082: 272 0.082 - 0.123: 99 0.123 - 0.165: 31 0.165 - 0.206: 6 Chirality restraints: 1194 Sorted by residual: chirality pdb=" CB ILE B 58 " pdb=" CA ILE B 58 " pdb=" CG1 ILE B 58 " pdb=" CG2 ILE B 58 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB ILE A 382 " pdb=" CA ILE A 382 " pdb=" CG1 ILE A 382 " pdb=" CG2 ILE A 382 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB ILE A 383 " pdb=" CA ILE A 383 " pdb=" CG1 ILE A 383 " pdb=" CG2 ILE A 383 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1191 not shown) Planarity restraints: 1275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.044 5.00e-02 4.00e+02 6.70e-02 7.17e+00 pdb=" N PRO B 236 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 82 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.85e+00 pdb=" C ALA R 82 " -0.045 2.00e-02 2.50e+03 pdb=" O ALA R 82 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA R 83 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 241 " 0.013 2.00e-02 2.50e+03 1.95e-02 6.62e+00 pdb=" CG PHE B 241 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE B 241 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 241 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE B 241 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 241 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 241 " -0.001 2.00e-02 2.50e+03 ... (remaining 1272 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2015 2.81 - 3.33: 6111 3.33 - 3.86: 12100 3.86 - 4.38: 14013 4.38 - 4.90: 25013 Nonbonded interactions: 59252 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.290 3.040 nonbonded pdb=" O ALA R 36 " pdb=" OG1 THR R 40 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.315 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.322 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.349 3.040 ... (remaining 59247 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.370 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 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 0.101 7496 Z= 0.242 Angle : 0.758 8.659 10232 Z= 0.432 Chirality : 0.051 0.206 1194 Planarity : 0.006 0.067 1275 Dihedral : 12.654 81.023 2485 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.14 % Allowed : 0.41 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.25), residues: 942 helix: -0.67 (0.24), residues: 352 sheet: 0.38 (0.34), residues: 211 loop : -0.97 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.020 0.002 TYR R 92 PHE 0.044 0.002 PHE B 241 TRP 0.018 0.002 TRP B 99 HIS 0.015 0.002 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.21 ( 7492) covalent geometry : angle 0.75693 / 0.43 (10226) SS BOND : bond 0.00345 / 0.17 ( 3) SS BOND : angle 2.03747 / 1.12 ( 6) hydrogen bonds : bond 0.14290 / 8.79 ( 383) hydrogen bonds : angle 6.65646 / 4.59 ( 1098) Misc. bond : bond 0.10119 / 6.32 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.303 Fit side-chains REVERT: A 272 ASP cc_start: 0.6554 (m-30) cc_final: 0.5659 (m-30) outliers start: 1 outliers final: 0 residues processed: 149 average time/residue: 0.4536 time to fit residues: 72.3558 Evaluate side-chains 108 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 45 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 67.423 > 50:) chunk 74 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN A 278 ASN ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 ASN R 73 ASN R 318 HIS B 75 GLN B 340 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.109598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.096877 restraints weight = 15743.757| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.59 r_work: 0.3321 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7496 Z= 0.137 Angle : 0.532 9.009 10232 Z= 0.290 Chirality : 0.043 0.196 1194 Planarity : 0.004 0.050 1275 Dihedral : 4.336 22.529 1034 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.06 % Allowed : 10.03 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.26), residues: 942 helix: 0.80 (0.26), residues: 367 sheet: 0.60 (0.33), residues: 208 loop : -0.77 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 313 TYR 0.011 0.001 TYR A 339 PHE 0.014 0.001 PHE R 264 TRP 0.012 0.001 TRP B 99 HIS 0.004 0.001 HIS R 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 7492) covalent geometry : angle 0.53098 / 0.29 (10226) SS BOND : bond 0.00279 / 0.14 ( 3) SS BOND : angle 1.27301 / 0.63 ( 6) hydrogen bonds : bond 0.04613 / 2.94 ( 383) hydrogen bonds : angle 4.78493 / 3.30 ( 1098) Misc. bond : bond 0.00065 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.357 Fit side-chains REVERT: A 29 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7588 (tm-30) REVERT: A 33 ASP cc_start: 0.8788 (m-30) cc_final: 0.8527 (m-30) REVERT: A 268 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7513 (tp30) REVERT: A 272 ASP cc_start: 0.7733 (m-30) cc_final: 0.7322 (m-30) REVERT: A 339 TYR cc_start: 0.8596 (m-80) cc_final: 0.8298 (m-80) REVERT: R 139 GLN cc_start: 0.9018 (tp40) cc_final: 0.8749 (mp10) REVERT: R 186 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6900 (tm-30) REVERT: N 50 ASP cc_start: 0.8077 (p0) cc_final: 0.7550 (p0) REVERT: N 53 GLN cc_start: 0.7177 (mp10) cc_final: 0.6908 (mp10) outliers start: 15 outliers final: 6 residues processed: 120 average time/residue: 0.4862 time to fit residues: 62.2333 Evaluate side-chains 104 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain R residue 186 GLU Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 89 optimal weight: 6.9990 chunk 55 optimal weight: 0.0040 chunk 81 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 GLN ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 318 HIS B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.111246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.098625 restraints weight = 15711.155| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.46 r_work: 0.3397 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7496 Z= 0.105 Angle : 0.492 8.712 10232 Z= 0.265 Chirality : 0.042 0.203 1194 Planarity : 0.003 0.044 1275 Dihedral : 4.009 20.164 1034 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.47 % Allowed : 11.68 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.27), residues: 942 helix: 1.54 (0.27), residues: 367 sheet: 0.78 (0.34), residues: 208 loop : -0.57 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 313 TYR 0.010 0.001 TYR A 339 PHE 0.011 0.001 PHE R 264 TRP 0.008 0.001 TRP R 261 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 7492) covalent geometry : angle 0.49115 / 0.27 (10226) SS BOND : bond 0.00267 / 0.14 ( 3) SS BOND : angle 1.04198 / 0.55 ( 6) hydrogen bonds : bond 0.03889 / 2.50 ( 383) hydrogen bonds : angle 4.41566 / 3.04 ( 1098) Misc. bond : bond 0.00045 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.285 Fit side-chains REVERT: A 268 GLU cc_start: 0.8505 (tm-30) cc_final: 0.7515 (tm-30) REVERT: A 272 ASP cc_start: 0.8042 (m-30) cc_final: 0.7407 (m-30) REVERT: R 139 GLN cc_start: 0.9098 (OUTLIER) cc_final: 0.8879 (mp10) REVERT: R 172 GLU cc_start: 0.7412 (tm-30) cc_final: 0.6975 (tm-30) REVERT: R 186 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6879 (tm-30) REVERT: R 190 LYS cc_start: 0.8119 (mttt) cc_final: 0.7911 (mttt) REVERT: B 243 THR cc_start: 0.8993 (p) cc_final: 0.8740 (p) REVERT: N 50 ASP cc_start: 0.8157 (p0) cc_final: 0.7661 (p0) REVERT: N 53 GLN cc_start: 0.7186 (mp10) cc_final: 0.6839 (mp10) outliers start: 18 outliers final: 8 residues processed: 126 average time/residue: 0.4704 time to fit residues: 63.3487 Evaluate side-chains 116 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 139 GLN Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 186 GLU Chi-restraints excluded: chain R residue 308 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 7 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 87 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 GLN ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 GLN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 318 HIS B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.110501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.097878 restraints weight = 16237.898| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.49 r_work: 0.3379 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7496 Z= 0.110 Angle : 0.489 8.902 10232 Z= 0.264 Chirality : 0.042 0.197 1194 Planarity : 0.003 0.042 1275 Dihedral : 3.928 19.114 1034 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.88 % Allowed : 13.19 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.28), residues: 942 helix: 1.82 (0.28), residues: 367 sheet: 0.88 (0.34), residues: 208 loop : -0.45 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 313 TYR 0.009 0.001 TYR A 339 PHE 0.012 0.001 PHE R 264 TRP 0.010 0.001 TRP R 55 HIS 0.003 0.001 HIS R 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 7492) covalent geometry : angle 0.48831 / 0.26 (10226) SS BOND : bond 0.00271 / 0.14 ( 3) SS BOND : angle 1.03941 / 0.56 ( 6) hydrogen bonds : bond 0.03880 / 2.49 ( 383) hydrogen bonds : angle 4.33704 / 3.00 ( 1098) Misc. bond : bond 0.00053 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.309 Fit side-chains REVERT: A 268 GLU cc_start: 0.8545 (tm-30) cc_final: 0.7516 (tm-30) REVERT: A 272 ASP cc_start: 0.8072 (m-30) cc_final: 0.7471 (m-30) REVERT: R 186 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6836 (tm-30) REVERT: B 243 THR cc_start: 0.8975 (p) cc_final: 0.8720 (p) REVERT: N 50 ASP cc_start: 0.8248 (p0) cc_final: 0.7724 (p0) REVERT: N 53 GLN cc_start: 0.7219 (mp10) cc_final: 0.6821 (mp10) outliers start: 21 outliers final: 9 residues processed: 122 average time/residue: 0.4764 time to fit residues: 62.1460 Evaluate side-chains 110 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 186 GLU Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 7 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 13 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 318 HIS B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.102932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.090100 restraints weight = 15944.245| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.55 r_work: 0.3218 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7496 Z= 0.221 Angle : 0.595 10.957 10232 Z= 0.321 Chirality : 0.046 0.198 1194 Planarity : 0.004 0.040 1275 Dihedral : 4.435 22.994 1034 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.30 % Allowed : 13.46 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.27), residues: 942 helix: 1.68 (0.28), residues: 365 sheet: 0.85 (0.35), residues: 200 loop : -0.45 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 313 TYR 0.012 0.001 TYR R 278 PHE 0.018 0.002 PHE R 264 TRP 0.010 0.001 TRP B 82 HIS 0.006 0.001 HIS R 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 ( 7492) covalent geometry : angle 0.59347 / 0.32 (10226) SS BOND : bond 0.00229 / 0.13 ( 3) SS BOND : angle 1.61440 / 0.93 ( 6) hydrogen bonds : bond 0.05155 / 3.29 ( 383) hydrogen bonds : angle 4.70681 / 3.29 ( 1098) Misc. bond : bond 0.00158 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.291 Fit side-chains REVERT: A 390 GLU cc_start: 0.8911 (tp30) cc_final: 0.8710 (tp30) REVERT: R 186 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6798 (tm-30) REVERT: N 50 ASP cc_start: 0.8539 (p0) cc_final: 0.7981 (p0) outliers start: 24 outliers final: 11 residues processed: 111 average time/residue: 0.4783 time to fit residues: 56.6844 Evaluate side-chains 104 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 186 GLU Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 GLN ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.107357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.094770 restraints weight = 16084.668| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.46 r_work: 0.3339 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7496 Z= 0.123 Angle : 0.529 8.730 10232 Z= 0.284 Chirality : 0.043 0.172 1194 Planarity : 0.003 0.038 1275 Dihedral : 4.188 25.305 1034 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.47 % Allowed : 14.97 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.28), residues: 942 helix: 1.88 (0.28), residues: 366 sheet: 0.75 (0.34), residues: 213 loop : -0.39 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 313 TYR 0.014 0.001 TYR R 278 PHE 0.014 0.001 PHE R 264 TRP 0.008 0.001 TRP R 261 HIS 0.003 0.001 HIS R 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 7492) covalent geometry : angle 0.52741 / 0.28 (10226) SS BOND : bond 0.00493 / 0.25 ( 3) SS BOND : angle 1.57525 / 1.01 ( 6) hydrogen bonds : bond 0.04185 / 2.69 ( 383) hydrogen bonds : angle 4.41727 / 3.07 ( 1098) Misc. bond : bond 0.00062 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.226 Fit side-chains REVERT: A 29 GLN cc_start: 0.8574 (tp40) cc_final: 0.8334 (tp-100) REVERT: A 33 ASP cc_start: 0.8967 (m-30) cc_final: 0.8751 (m-30) REVERT: A 268 GLU cc_start: 0.8609 (tm-30) cc_final: 0.7955 (tp30) REVERT: A 272 ASP cc_start: 0.8245 (m-30) cc_final: 0.7955 (m-30) REVERT: R 186 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6758 (tm-30) REVERT: N 50 ASP cc_start: 0.8386 (p0) cc_final: 0.7877 (p0) outliers start: 18 outliers final: 10 residues processed: 112 average time/residue: 0.4462 time to fit residues: 53.7313 Evaluate side-chains 108 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 186 GLU Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 15 optimal weight: 0.0870 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 47 optimal weight: 0.0270 chunk 26 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.108379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.095940 restraints weight = 16029.596| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.48 r_work: 0.3320 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7496 Z= 0.102 Angle : 0.508 8.167 10232 Z= 0.271 Chirality : 0.042 0.189 1194 Planarity : 0.003 0.037 1275 Dihedral : 3.905 21.634 1034 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.92 % Allowed : 15.93 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.28), residues: 942 helix: 2.06 (0.28), residues: 367 sheet: 0.89 (0.34), residues: 214 loop : -0.28 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 313 TYR 0.015 0.001 TYR R 278 PHE 0.016 0.001 PHE A 212 TRP 0.009 0.001 TRP R 261 HIS 0.002 0.000 HIS R 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 ( 7492) covalent geometry : angle 0.50731 / 0.27 (10226) SS BOND : bond 0.00076 / 0.04 ( 3) SS BOND : angle 1.26011 / 0.81 ( 6) hydrogen bonds : bond 0.03645 / 2.36 ( 383) hydrogen bonds : angle 4.23441 / 2.93 ( 1098) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.296 Fit side-chains REVERT: A 29 GLN cc_start: 0.8522 (tp40) cc_final: 0.7914 (tm-30) REVERT: A 268 GLU cc_start: 0.8578 (tm-30) cc_final: 0.7687 (tp30) REVERT: A 272 ASP cc_start: 0.8216 (m-30) cc_final: 0.7703 (m-30) REVERT: R 186 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6780 (tm-30) REVERT: B 243 THR cc_start: 0.8993 (p) cc_final: 0.8720 (p) REVERT: N 50 ASP cc_start: 0.8256 (p0) cc_final: 0.7742 (p0) outliers start: 14 outliers final: 8 residues processed: 119 average time/residue: 0.4667 time to fit residues: 59.5109 Evaluate side-chains 106 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 186 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 50 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 43 optimal weight: 0.2980 chunk 46 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.106759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.094265 restraints weight = 16169.526| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.49 r_work: 0.3295 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7496 Z= 0.125 Angle : 0.546 10.018 10232 Z= 0.290 Chirality : 0.043 0.186 1194 Planarity : 0.003 0.037 1275 Dihedral : 3.988 21.863 1034 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.06 % Allowed : 16.48 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.28), residues: 942 helix: 2.05 (0.28), residues: 367 sheet: 1.07 (0.34), residues: 209 loop : -0.34 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 313 TYR 0.015 0.001 TYR R 278 PHE 0.014 0.001 PHE R 264 TRP 0.008 0.001 TRP R 261 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 7492) covalent geometry : angle 0.54506 / 0.29 (10226) SS BOND : bond 0.00178 / 0.09 ( 3) SS BOND : angle 1.29068 / 0.81 ( 6) hydrogen bonds : bond 0.03971 / 2.56 ( 383) hydrogen bonds : angle 4.30400 / 2.99 ( 1098) Misc. bond : bond 0.00068 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.303 Fit side-chains REVERT: A 33 ASP cc_start: 0.8908 (m-30) cc_final: 0.8682 (m-30) REVERT: A 268 GLU cc_start: 0.8623 (tm-30) cc_final: 0.7710 (tp30) REVERT: A 272 ASP cc_start: 0.8249 (m-30) cc_final: 0.7717 (m-30) REVERT: R 186 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.6763 (tm-30) REVERT: N 50 ASP cc_start: 0.8319 (p0) cc_final: 0.7812 (p0) outliers start: 15 outliers final: 10 residues processed: 109 average time/residue: 0.4387 time to fit residues: 51.6111 Evaluate side-chains 111 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 186 GLU Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 21 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.105295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.092811 restraints weight = 16071.208| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.49 r_work: 0.3297 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7496 Z= 0.199 Angle : 0.610 11.182 10232 Z= 0.328 Chirality : 0.045 0.209 1194 Planarity : 0.003 0.037 1275 Dihedral : 4.380 23.319 1034 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.92 % Allowed : 16.76 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.28), residues: 942 helix: 1.89 (0.28), residues: 366 sheet: 1.00 (0.34), residues: 210 loop : -0.40 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.020 0.001 TYR R 278 PHE 0.017 0.002 PHE R 264 TRP 0.007 0.001 TRP B 339 HIS 0.006 0.001 HIS R 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 ( 7492) covalent geometry : angle 0.60926 / 0.33 (10226) SS BOND : bond 0.00217 / 0.12 ( 3) SS BOND : angle 1.50058 / 0.92 ( 6) hydrogen bonds : bond 0.04836 / 3.11 ( 383) hydrogen bonds : angle 4.59205 / 3.21 ( 1098) Misc. bond : bond 0.00139 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.280 Fit side-chains REVERT: A 213 GLN cc_start: 0.8570 (tp-100) cc_final: 0.8334 (tp40) REVERT: R 186 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6676 (tm-30) REVERT: N 50 ASP cc_start: 0.8508 (p0) cc_final: 0.7965 (p0) outliers start: 14 outliers final: 10 residues processed: 106 average time/residue: 0.4507 time to fit residues: 51.3599 Evaluate side-chains 108 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 186 GLU Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 47 optimal weight: 0.0970 chunk 73 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.104442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.092338 restraints weight = 16183.897| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.35 r_work: 0.3256 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7496 Z= 0.158 Angle : 0.588 10.428 10232 Z= 0.316 Chirality : 0.044 0.186 1194 Planarity : 0.003 0.037 1275 Dihedral : 4.318 22.562 1034 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.92 % Allowed : 17.31 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.27), residues: 942 helix: 1.92 (0.27), residues: 365 sheet: 1.02 (0.34), residues: 209 loop : -0.40 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 313 TYR 0.019 0.001 TYR R 278 PHE 0.016 0.001 PHE A 212 TRP 0.007 0.001 TRP B 82 HIS 0.004 0.001 HIS R 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 7492) covalent geometry : angle 0.58695 / 0.32 (10226) SS BOND : bond 0.00145 / 0.08 ( 3) SS BOND : angle 1.41862 / 0.88 ( 6) hydrogen bonds : bond 0.04521 / 2.91 ( 383) hydrogen bonds : angle 4.50310 / 3.14 ( 1098) Misc. bond : bond 0.00092 / 0.06 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.307 Fit side-chains REVERT: A 213 GLN cc_start: 0.8506 (tp-100) cc_final: 0.8251 (tp40) REVERT: R 186 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.6695 (tm-30) REVERT: N 50 ASP cc_start: 0.8473 (p0) cc_final: 0.7950 (p0) outliers start: 14 outliers final: 12 residues processed: 106 average time/residue: 0.4389 time to fit residues: 50.0487 Evaluate side-chains 113 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 186 GLU Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 56 optimal weight: 0.0470 chunk 21 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 86 optimal weight: 0.0570 chunk 30 optimal weight: 0.0370 chunk 87 optimal weight: 5.9990 overall best weight: 0.3674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 318 HIS B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.108870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.096882 restraints weight = 16024.949| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.36 r_work: 0.3334 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7496 Z= 0.107 Angle : 0.539 11.323 10232 Z= 0.286 Chirality : 0.042 0.180 1194 Planarity : 0.003 0.037 1275 Dihedral : 3.959 21.371 1034 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.24 % Allowed : 17.99 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.28), residues: 942 helix: 2.08 (0.28), residues: 366 sheet: 1.07 (0.34), residues: 209 loop : -0.32 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 232 TYR 0.022 0.001 TYR R 278 PHE 0.014 0.001 PHE A 212 TRP 0.010 0.001 TRP R 261 HIS 0.003 0.000 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 7492) covalent geometry : angle 0.53845 / 0.29 (10226) SS BOND : bond 0.00078 / 0.04 ( 3) SS BOND : angle 1.23133 / 0.78 ( 6) hydrogen bonds : bond 0.03604 / 2.35 ( 383) hydrogen bonds : angle 4.26087 / 2.95 ( 1098) Misc. bond : bond 0.00024 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2571.12 seconds wall clock time: 44 minutes 33.92 seconds (2673.92 seconds total)