Starting phenix.real_space_refine on Wed Aug 5 17:55:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jrv_36607/08_2026/8jrv_36607.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jrv_36607/08_2026/8jrv_36607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jrv_36607/08_2026/8jrv_36607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jrv_36607/08_2026/8jrv_36607.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jrv_36607/08_2026/8jrv_36607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jrv_36607/08_2026/8jrv_36607.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8jrv_36607/08_2026/8jrv_36607.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jrv_36607/08_2026/8jrv_36607.cif" } resolution = 3.3 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= 0.006 sd= 0.059 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 4023 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 21 5.16 5 C 4933 2.51 5 N 1307 2.21 5 O 1438 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7707 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2338 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 5, 'TRANS': 313} Chain breaks: 4 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 341 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'PHE:plan': 5, 'GLU:plan': 6, 'TRP:plan': 3, 'TYR:plan': 1, 'ASP:plan': 4, 'HIS:plan': 3, 'ARG:plan': 5, 'ASN:plan1': 1, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 164 Chain: "G" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 168 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 24} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 2632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2632 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 28, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 14, 'ARG:plan': 5, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 111 Chain: "H" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 886 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 788 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 855 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 110} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 1.77, per 1000 atoms: 0.23 Number of scatterers: 7707 At special positions: 0 Unit cell: (96.39, 97.461, 164.934, 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 21 16.00 P 8 15.00 O 1438 8.00 N 1307 7.00 C 4933 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 224 " - pdb=" SG CYS R 294 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 382.4 milliseconds 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1936 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 13 sheets defined 30.7% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'R' and resid 27 through 47 Processing helix chain 'R' and resid 128 through 166 removed outlier: 3.727A pdb=" N SER R 140 " --> pdb=" O LYS R 136 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR R 145 " --> pdb=" O PHE R 141 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY R 148 " --> pdb=" O MET R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 170 removed outlier: 3.946A pdb=" N HIS R 170 " --> pdb=" O SER R 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 167 through 170' Processing helix chain 'R' and resid 171 through 207 removed outlier: 4.463A pdb=" N HIS R 177 " --> pdb=" O ARG R 173 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA R 178 " --> pdb=" O ASN R 174 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER R 183 " --> pdb=" O ASN R 179 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE R 184 " --> pdb=" O LEU R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 254 removed outlier: 3.543A pdb=" N TYR R 239 " --> pdb=" O ILE R 235 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU R 242 " --> pdb=" O ASN R 238 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN R 251 " --> pdb=" O LEU R 247 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU R 252 " --> pdb=" O TYR R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 272 removed outlier: 3.562A pdb=" N LEU R 268 " --> pdb=" O PHE R 264 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY R 269 " --> pdb=" O SER R 265 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP R 272 " --> pdb=" O LEU R 268 " (cutoff:3.500A) Processing helix chain 'R' and resid 273 through 278 removed outlier: 3.908A pdb=" N LEU R 277 " --> pdb=" O GLY R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 288 removed outlier: 3.666A pdb=" N CYS R 287 " --> pdb=" O ALA R 283 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 337 Proline residue: R 310 - end of helix removed outlier: 4.174A pdb=" N ARG R 334 " --> pdb=" O VAL R 330 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ALA R 335 " --> pdb=" O ALA R 331 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG R 336 " --> pdb=" O LYS R 332 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN R 337 " --> pdb=" O LEU R 333 " (cutoff:3.500A) Processing helix chain 'R' and resid 342 through 367 removed outlier: 3.859A pdb=" N ARG R 346 " --> pdb=" O ASP R 342 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA R 348 " --> pdb=" O LYS R 344 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR R 353 " --> pdb=" O LYS R 349 " (cutoff:3.500A) Proline residue: R 356 - end of helix removed outlier: 3.551A pdb=" N HIS R 361 " --> pdb=" O LEU R 357 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU R 362 " --> pdb=" O LEU R 358 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL R 363 " --> pdb=" O GLY R 359 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE R 365 " --> pdb=" O HIS R 361 " (cutoff:3.500A) Processing helix chain 'R' and resid 380 through 391 removed outlier: 3.675A pdb=" N PHE R 391 " --> pdb=" O PHE R 387 " (cutoff:3.500A) Processing helix chain 'R' and resid 391 through 402 Processing helix chain 'R' and resid 404 through 425 removed outlier: 3.505A pdb=" N ARG R 414 " --> pdb=" O GLU R 410 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS R 422 " --> pdb=" O TRP R 418 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL R 423 " --> pdb=" O ARG R 419 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 25 removed outlier: 3.582A pdb=" N PHE G 6 " --> pdb=" O SER G 2 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER G 11 " --> pdb=" O THR G 7 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR G 13 " --> pdb=" O ASP G 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.617A pdb=" N LYS A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'B' and resid 61 through 64 Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing sheet with id=AA1, first strand: chain 'R' and resid 1360 through 1364 removed outlier: 3.756A pdb=" N SEP R1363 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 20 " --> pdb=" O LYS A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28 removed outlier: 5.764A pdb=" N PHE A 27 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 148 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP A 143 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 60 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA A 59 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 77 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 28 removed outlier: 5.764A pdb=" N PHE A 27 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 148 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA5, first strand: chain 'A' and resid 183 through 188 removed outlier: 3.939A pdb=" N ALA A 201 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR A 186 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 199 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 197 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS A 198 " --> pdb=" O THR A 221 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 207 through 208 removed outlier: 3.556A pdb=" N VAL A 325 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL A 328 " --> pdb=" O LYS A 230 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS A 230 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 258 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLN A 237 " --> pdb=" O PRO A 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 8 through 10 Processing sheet with id=AA8, first strand: chain 'H' and resid 60 through 63 removed outlier: 7.156A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB1, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.719A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 20 through 21 removed outlier: 3.521A pdb=" N VAL L 20 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.734A pdb=" N THR B 77 " --> pdb=" O ASP B 72 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP B 72 " --> pdb=" O THR B 77 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.574A pdb=" N VAL B 12 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR B 108 " --> pdb=" O TYR B 93 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG B 38 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B 58 " --> pdb=" O SER B 50 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 984 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: 1.18 Time building geometry restraints manager: 0.85 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: 1354 1.33 - 1.45: 2110 1.45 - 1.58: 4364 1.58 - 1.70: 23 1.70 - 1.82: 28 Bond restraints: 7879 Sorted by residual: bond pdb=" OG1 TPO R1360 " pdb=" P TPO R1360 " ideal model delta sigma weight residual 1.717 1.619 0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" O1P TPO R1360 " pdb=" P TPO R1360 " ideal model delta sigma weight residual 1.525 1.612 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" O3P TPO R1360 " pdb=" P TPO R1360 " ideal model delta sigma weight residual 1.528 1.612 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" C1B PIO A 701 " pdb=" O3C PIO A 701 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" O13 PIO A 701 " pdb=" P1 PIO A 701 " ideal model delta sigma weight residual 1.651 1.589 0.062 2.00e-02 2.50e+03 9.51e+00 ... (remaining 7874 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 10668 3.04 - 6.09: 76 6.09 - 9.13: 20 9.13 - 12.17: 3 12.17 - 15.21: 3 Bond angle restraints: 10770 Sorted by residual: angle pdb=" C2C PIO A 701 " pdb=" C1C PIO A 701 " pdb=" O13 PIO A 701 " ideal model delta sigma weight residual 108.14 92.93 15.21 3.00e+00 1.11e-01 2.57e+01 angle pdb=" N ILE R 270 " pdb=" CA ILE R 270 " pdb=" C ILE R 270 " ideal model delta sigma weight residual 113.53 109.00 4.53 9.80e-01 1.04e+00 2.13e+01 angle pdb=" C5 PIO A 701 " pdb=" C4 PIO A 701 " pdb=" O4 PIO A 701 " ideal model delta sigma weight residual 109.61 96.34 13.27 3.00e+00 1.11e-01 1.96e+01 angle pdb=" C5 PIO A 701 " pdb=" O5 PIO A 701 " pdb=" P5 PIO A 701 " ideal model delta sigma weight residual 123.85 136.56 -12.71 3.00e+00 1.11e-01 1.80e+01 angle pdb=" OG1 TPO R1360 " pdb=" P TPO R1360 " pdb=" O1P TPO R1360 " ideal model delta sigma weight residual 100.43 112.41 -11.98 3.00e+00 1.11e-01 1.59e+01 ... (remaining 10765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4205 17.95 - 35.91: 299 35.91 - 53.86: 72 53.86 - 71.81: 11 71.81 - 89.77: 6 Dihedral angle restraints: 4593 sinusoidal: 1584 harmonic: 3009 Sorted by residual: dihedral pdb=" CB CYS L 24 " pdb=" SG CYS L 24 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 166.90 -73.90 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CA VAL R 292 " pdb=" C VAL R 292 " pdb=" N GLN R 293 " pdb=" CA GLN R 293 " ideal model delta harmonic sigma weight residual 180.00 157.72 22.28 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA LEU A 191 " pdb=" C LEU A 191 " pdb=" N MET A 192 " pdb=" CA MET A 192 " ideal model delta harmonic sigma weight residual 180.00 -160.74 -19.26 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 4590 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1128 0.063 - 0.126: 125 0.126 - 0.189: 5 0.189 - 0.253: 0 0.253 - 0.316: 3 Chirality restraints: 1261 Sorted by residual: chirality pdb=" C4 PIO A 701 " pdb=" C3 PIO A 701 " pdb=" C5 PIO A 701 " pdb=" O4 PIO A 701 " both_signs ideal model delta sigma weight residual False 2.50 2.82 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" C1 PIO A 701 " pdb=" C2 PIO A 701 " pdb=" C6 PIO A 701 " pdb=" O1 PIO A 701 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" C2C PIO A 701 " pdb=" C1C PIO A 701 " pdb=" C3C PIO A 701 " pdb=" O2C PIO A 701 " both_signs ideal model delta sigma weight residual False -2.56 -2.30 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 1258 not shown) Planarity restraints: 1356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 258 " -0.030 5.00e-02 4.00e+02 4.48e-02 3.22e+00 pdb=" N PRO R 259 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO R 259 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 259 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 88 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO A 89 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 89 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 89 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 274 " -0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO R 275 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 275 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 275 " -0.018 5.00e-02 4.00e+02 ... (remaining 1353 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1593 2.78 - 3.31: 7251 3.31 - 3.84: 12045 3.84 - 4.37: 13113 4.37 - 4.90: 23189 Nonbonded interactions: 57191 Sorted by model distance: nonbonded pdb=" O MET B 82 " pdb=" ND2 ASN B 83 " model vdw 2.250 3.120 nonbonded pdb=" OD2 ASP A 204 " pdb=" OG SER A 215 " model vdw 2.275 3.040 nonbonded pdb=" NH1 ARG H 70 " pdb=" O SER H 88 " model vdw 2.294 3.120 nonbonded pdb=" O2P SEP R1363 " pdb=" OH TYR A 21 " model vdw 2.295 3.040 nonbonded pdb=" OD2 ASP A 297 " pdb=" OH TYR H 60 " model vdw 2.315 3.040 ... (remaining 57186 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.580 Find NCS groups from input model: 0.050 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 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 : 0.003 0.098 7882 Z= 0.168 Angle : 0.713 15.214 10776 Z= 0.314 Chirality : 0.041 0.316 1261 Planarity : 0.004 0.045 1356 Dihedral : 13.514 89.766 2648 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: -0.16 (0.27), residues: 1005 helix: 0.79 (0.30), residues: 272 sheet: 0.43 (0.32), residues: 286 loop : -0.99 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 90 TYR 0.007 0.001 TYR B 37 PHE 0.023 0.001 PHE R 289 TRP 0.011 0.001 TRP R 241 HIS 0.002 0.000 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 ( 7879) covalent geometry : angle 0.71303 / 0.31 (10770) SS BOND : bond 0.00091 / 0.05 ( 3) SS BOND : angle 1.05046 / 0.60 ( 6) hydrogen bonds : bond 0.28496 / 20.23 ( 347) hydrogen bonds : angle 9.12027 / 6.82 ( 984) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.298 Fit side-chains REVERT: R 141 PHE cc_start: 0.7678 (m-80) cc_final: 0.7256 (m-80) REVERT: R 197 LEU cc_start: 0.8448 (mt) cc_final: 0.8213 (mt) REVERT: R 232 GLN cc_start: 0.8355 (mm-40) cc_final: 0.8087 (mm110) REVERT: A 122 ASN cc_start: 0.8646 (t0) cc_final: 0.8398 (t0) REVERT: A 145 GLU cc_start: 0.7606 (tt0) cc_final: 0.7061 (tt0) REVERT: A 185 GLU cc_start: 0.6350 (tp30) cc_final: 0.6109 (tp30) REVERT: A 222 ASN cc_start: 0.7441 (t160) cc_final: 0.6976 (t0) REVERT: A 225 ASN cc_start: 0.7988 (p0) cc_final: 0.7773 (p0) REVERT: A 255 MET cc_start: 0.7163 (tmm) cc_final: 0.6930 (tmm) REVERT: L 12 LEU cc_start: 0.8417 (mm) cc_final: 0.8087 (mm) REVERT: B 46 GLU cc_start: 0.6164 (pp20) cc_final: 0.5906 (pp20) REVERT: B 65 ASP cc_start: 0.8393 (t0) cc_final: 0.7823 (t0) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.0824 time to fit residues: 29.3185 Evaluate side-chains 222 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.0570 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 318 ASN A 219 HIS ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.093742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.083200 restraints weight = 20524.338| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.07 r_work: 0.3206 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7882 Z= 0.170 Angle : 0.659 8.638 10776 Z= 0.345 Chirality : 0.042 0.180 1261 Planarity : 0.004 0.037 1356 Dihedral : 5.285 56.468 1137 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.87 % Allowed : 12.17 % Favored : 85.96 % 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: -0.09 (0.27), residues: 1005 helix: 0.98 (0.29), residues: 281 sheet: 0.30 (0.30), residues: 308 loop : -1.01 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 45 TYR 0.013 0.001 TYR B 79 PHE 0.019 0.002 PHE R 263 TRP 0.039 0.002 TRP B 104 HIS 0.005 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 7879) covalent geometry : angle 0.65829 / 0.34 (10770) SS BOND : bond 0.00214 / 0.11 ( 3) SS BOND : angle 1.60182 / 0.92 ( 6) hydrogen bonds : bond 0.05483 / 3.85 ( 347) hydrogen bonds : angle 6.08768 / 4.45 ( 984) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 237 time to evaluate : 0.309 Fit side-chains REVERT: R 131 GLN cc_start: 0.7023 (mp10) cc_final: 0.6441 (mp10) REVERT: R 141 PHE cc_start: 0.7838 (m-80) cc_final: 0.7396 (m-80) REVERT: R 225 ARG cc_start: 0.6421 (ttp-170) cc_final: 0.6034 (mtm110) REVERT: R 391 PHE cc_start: 0.8662 (m-10) cc_final: 0.8433 (m-80) REVERT: R 419 ARG cc_start: 0.8491 (ttt90) cc_final: 0.8201 (tpt170) REVERT: A 122 ASN cc_start: 0.9062 (t0) cc_final: 0.8749 (t0) REVERT: A 222 ASN cc_start: 0.7900 (t0) cc_final: 0.7298 (t0) REVERT: A 225 ASN cc_start: 0.8108 (p0) cc_final: 0.7804 (p0) REVERT: A 256 GLU cc_start: 0.8457 (tp30) cc_final: 0.8137 (tp30) REVERT: B 34 MET cc_start: 0.8182 (mmm) cc_final: 0.7953 (mmm) REVERT: B 63 VAL cc_start: 0.8287 (t) cc_final: 0.7869 (p) outliers start: 14 outliers final: 12 residues processed: 245 average time/residue: 0.0842 time to fit residues: 28.4927 Evaluate side-chains 235 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 223 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain H residue 80 ASN Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 0.0980 chunk 10 optimal weight: 0.0270 chunk 79 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS H 80 ASN ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.092858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.082284 restraints weight = 20543.948| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.06 r_work: 0.3190 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7882 Z= 0.139 Angle : 0.621 8.815 10776 Z= 0.321 Chirality : 0.041 0.177 1261 Planarity : 0.004 0.039 1356 Dihedral : 5.202 58.565 1137 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.61 % Allowed : 16.18 % Favored : 80.21 % 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: -0.08 (0.27), residues: 1005 helix: 1.22 (0.30), residues: 281 sheet: 0.12 (0.30), residues: 324 loop : -1.07 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 45 TYR 0.020 0.001 TYR R 145 PHE 0.025 0.001 PHE G 6 TRP 0.027 0.001 TRP B 104 HIS 0.014 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 7879) covalent geometry : angle 0.62026 / 0.32 (10770) SS BOND : bond 0.00457 / 0.22 ( 3) SS BOND : angle 1.37536 / 0.80 ( 6) hydrogen bonds : bond 0.04807 / 3.37 ( 347) hydrogen bonds : angle 5.65845 / 4.12 ( 984) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 241 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: R 131 GLN cc_start: 0.7181 (mp10) cc_final: 0.6732 (mp10) REVERT: R 141 PHE cc_start: 0.7784 (m-80) cc_final: 0.7356 (m-80) REVERT: R 225 ARG cc_start: 0.6067 (ttp-170) cc_final: 0.5791 (mmt-90) REVERT: R 304 TRP cc_start: 0.8295 (m-10) cc_final: 0.7875 (m-10) REVERT: R 419 ARG cc_start: 0.8508 (ttt90) cc_final: 0.8194 (tpt170) REVERT: A 83 ASN cc_start: 0.8672 (m-40) cc_final: 0.8439 (t0) REVERT: A 122 ASN cc_start: 0.9095 (t0) cc_final: 0.8781 (t0) REVERT: A 222 ASN cc_start: 0.7720 (t0) cc_final: 0.7131 (t0) REVERT: A 225 ASN cc_start: 0.8202 (p0) cc_final: 0.7917 (p0) REVERT: A 256 GLU cc_start: 0.8427 (tp30) cc_final: 0.8118 (tp30) REVERT: A 257 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7437 (mm-30) REVERT: H 60 TYR cc_start: 0.8176 (m-10) cc_final: 0.7967 (m-10) REVERT: H 85 GLN cc_start: 0.8348 (tp40) cc_final: 0.8122 (mm110) REVERT: B 63 VAL cc_start: 0.8139 (t) cc_final: 0.7711 (p) REVERT: B 83 ASN cc_start: 0.8415 (m110) cc_final: 0.8125 (m110) outliers start: 27 outliers final: 23 residues processed: 253 average time/residue: 0.0783 time to fit residues: 27.6535 Evaluate side-chains 255 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 232 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 179 ASN Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain R residue 394 LEU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain H residue 80 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 111 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 26 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 53 optimal weight: 0.2980 chunk 81 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 298 ASN A 219 HIS ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.091938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.081253 restraints weight = 20522.986| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.03 r_work: 0.3167 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7882 Z= 0.151 Angle : 0.630 9.013 10776 Z= 0.323 Chirality : 0.041 0.174 1261 Planarity : 0.004 0.039 1356 Dihedral : 5.122 58.531 1137 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.28 % Allowed : 20.05 % Favored : 75.67 % 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: -0.05 (0.27), residues: 1005 helix: 1.08 (0.30), residues: 288 sheet: 0.13 (0.29), residues: 328 loop : -0.95 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 45 TYR 0.012 0.001 TYR H 107 PHE 0.026 0.002 PHE G 6 TRP 0.018 0.001 TRP B 104 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 7879) covalent geometry : angle 0.62913 / 0.32 (10770) SS BOND : bond 0.00074 / 0.04 ( 3) SS BOND : angle 1.57310 / 0.92 ( 6) hydrogen bonds : bond 0.04370 / 3.07 ( 347) hydrogen bonds : angle 5.42495 / 3.93 ( 984) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 245 time to evaluate : 0.295 Fit side-chains REVERT: R 131 GLN cc_start: 0.7249 (mp10) cc_final: 0.6795 (mp10) REVERT: R 141 PHE cc_start: 0.7898 (m-80) cc_final: 0.7384 (m-80) REVERT: R 152 SER cc_start: 0.9018 (p) cc_final: 0.8810 (p) REVERT: R 225 ARG cc_start: 0.5975 (ttp-170) cc_final: 0.5766 (mmt-90) REVERT: R 304 TRP cc_start: 0.8451 (OUTLIER) cc_final: 0.7997 (m-10) REVERT: R 406 GLU cc_start: 0.8006 (mp0) cc_final: 0.7803 (mp0) REVERT: R 419 ARG cc_start: 0.8580 (ttt90) cc_final: 0.8236 (tpt170) REVERT: A 83 ASN cc_start: 0.8629 (m-40) cc_final: 0.8343 (t0) REVERT: A 122 ASN cc_start: 0.9131 (t0) cc_final: 0.8822 (t0) REVERT: A 222 ASN cc_start: 0.7814 (t0) cc_final: 0.7517 (t0) REVERT: A 225 ASN cc_start: 0.8413 (p0) cc_final: 0.8111 (p0) REVERT: A 256 GLU cc_start: 0.8501 (tp30) cc_final: 0.8292 (tp30) REVERT: A 257 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7458 (mm-30) REVERT: A 297 ASP cc_start: 0.8408 (p0) cc_final: 0.8157 (p0) REVERT: H 60 TYR cc_start: 0.8202 (m-10) cc_final: 0.7981 (m-10) REVERT: H 85 GLN cc_start: 0.8306 (tp40) cc_final: 0.8066 (mm110) REVERT: B 3 GLN cc_start: 0.8690 (pm20) cc_final: 0.8463 (pm20) REVERT: B 43 LYS cc_start: 0.9392 (mmtt) cc_final: 0.9078 (mmtp) REVERT: B 63 VAL cc_start: 0.8177 (t) cc_final: 0.7778 (p) REVERT: B 82 MET cc_start: 0.8057 (mmt) cc_final: 0.7810 (mmt) REVERT: B 83 ASN cc_start: 0.8467 (m110) cc_final: 0.8171 (m110) REVERT: B 88 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8532 (pm20) outliers start: 32 outliers final: 25 residues processed: 259 average time/residue: 0.0641 time to fit residues: 23.5383 Evaluate side-chains 259 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 232 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 179 ASN Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 304 TRP Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain R residue 394 LEU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 424 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain H residue 80 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 111 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN B 83 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.091550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.080791 restraints weight = 20569.620| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.09 r_work: 0.3159 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7882 Z= 0.139 Angle : 0.644 9.471 10776 Z= 0.320 Chirality : 0.041 0.172 1261 Planarity : 0.004 0.039 1356 Dihedral : 5.062 58.461 1137 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 5.48 % Allowed : 20.05 % Favored : 74.47 % 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: -0.03 (0.27), residues: 1005 helix: 1.24 (0.30), residues: 288 sheet: 0.05 (0.30), residues: 323 loop : -0.95 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 67 TYR 0.011 0.001 TYR H 107 PHE 0.028 0.002 PHE A 268 TRP 0.013 0.001 TRP R 304 HIS 0.006 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 7879) covalent geometry : angle 0.64281 / 0.32 (10770) SS BOND : bond 0.00103 / 0.05 ( 3) SS BOND : angle 1.48484 / 0.87 ( 6) hydrogen bonds : bond 0.04115 / 2.88 ( 347) hydrogen bonds : angle 5.31371 / 3.84 ( 984) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 239 time to evaluate : 0.250 Fit side-chains REVERT: R 131 GLN cc_start: 0.7256 (mp10) cc_final: 0.6826 (mp10) REVERT: R 141 PHE cc_start: 0.7906 (m-80) cc_final: 0.7340 (m-80) REVERT: R 152 SER cc_start: 0.9026 (p) cc_final: 0.8810 (p) REVERT: R 225 ARG cc_start: 0.5996 (ttp-170) cc_final: 0.5661 (mtt90) REVERT: R 304 TRP cc_start: 0.8383 (OUTLIER) cc_final: 0.7987 (m-10) REVERT: R 352 LEU cc_start: 0.8864 (mm) cc_final: 0.8461 (mm) REVERT: R 419 ARG cc_start: 0.8569 (ttt90) cc_final: 0.8255 (tpt170) REVERT: A 83 ASN cc_start: 0.8552 (m-40) cc_final: 0.8221 (t0) REVERT: A 122 ASN cc_start: 0.9141 (t0) cc_final: 0.8854 (t0) REVERT: A 222 ASN cc_start: 0.7878 (t0) cc_final: 0.7583 (t0) REVERT: A 225 ASN cc_start: 0.8468 (p0) cc_final: 0.8159 (p0) REVERT: A 232 LYS cc_start: 0.8810 (tppp) cc_final: 0.8471 (tppp) REVERT: A 256 GLU cc_start: 0.8551 (tp30) cc_final: 0.8259 (tp30) REVERT: A 257 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7312 (mm-30) REVERT: A 297 ASP cc_start: 0.8413 (p0) cc_final: 0.8168 (p0) REVERT: A 346 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8485 (mm-30) REVERT: H 60 TYR cc_start: 0.8185 (m-10) cc_final: 0.7959 (m-10) REVERT: H 85 GLN cc_start: 0.8329 (tp40) cc_final: 0.8090 (mm110) REVERT: H 90 ARG cc_start: 0.8665 (ptp-110) cc_final: 0.8188 (ptp-170) REVERT: L 37 TYR cc_start: 0.9038 (m-80) cc_final: 0.8638 (m-80) REVERT: L 83 ASP cc_start: 0.8322 (m-30) cc_final: 0.8121 (m-30) REVERT: B 20 LEU cc_start: 0.8657 (mm) cc_final: 0.8429 (mm) REVERT: B 43 LYS cc_start: 0.9309 (mmtt) cc_final: 0.9043 (mmtp) REVERT: B 63 VAL cc_start: 0.8112 (OUTLIER) cc_final: 0.7673 (p) REVERT: B 77 THR cc_start: 0.8371 (p) cc_final: 0.8138 (p) REVERT: B 81 GLN cc_start: 0.7581 (tp40) cc_final: 0.7347 (tp40) REVERT: B 82 MET cc_start: 0.8214 (mmt) cc_final: 0.7548 (mmt) REVERT: B 83 ASN cc_start: 0.8605 (m-40) cc_final: 0.8209 (m110) outliers start: 41 outliers final: 32 residues processed: 255 average time/residue: 0.0646 time to fit residues: 22.8939 Evaluate side-chains 266 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 232 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 179 ASN Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 304 TRP Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain R residue 394 LEU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 424 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain H residue 80 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 111 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 2.9990 chunk 22 optimal weight: 0.0470 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 69 optimal weight: 0.0370 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.092058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.081295 restraints weight = 20575.176| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.09 r_work: 0.3169 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7882 Z= 0.126 Angle : 0.631 8.825 10776 Z= 0.315 Chirality : 0.040 0.170 1261 Planarity : 0.004 0.039 1356 Dihedral : 4.989 58.247 1137 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.14 % Allowed : 22.19 % Favored : 73.66 % 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: -0.00 (0.27), residues: 1005 helix: 1.33 (0.31), residues: 288 sheet: 0.00 (0.30), residues: 323 loop : -0.93 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 66 TYR 0.010 0.001 TYR G 10 PHE 0.028 0.002 PHE G 6 TRP 0.014 0.001 TRP R 304 HIS 0.006 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 7879) covalent geometry : angle 0.63004 / 0.32 (10770) SS BOND : bond 0.00208 / 0.10 ( 3) SS BOND : angle 1.37452 / 0.80 ( 6) hydrogen bonds : bond 0.03876 / 2.71 ( 347) hydrogen bonds : angle 5.15508 / 3.72 ( 984) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 240 time to evaluate : 0.176 Fit side-chains REVERT: R 131 GLN cc_start: 0.7245 (mp10) cc_final: 0.6813 (mp10) REVERT: R 141 PHE cc_start: 0.7913 (m-80) cc_final: 0.7310 (m-80) REVERT: R 152 SER cc_start: 0.9009 (p) cc_final: 0.8799 (p) REVERT: R 304 TRP cc_start: 0.8445 (OUTLIER) cc_final: 0.8014 (m-10) REVERT: R 352 LEU cc_start: 0.8881 (mm) cc_final: 0.8508 (mm) REVERT: R 419 ARG cc_start: 0.8571 (ttt90) cc_final: 0.8262 (tpt170) REVERT: A 83 ASN cc_start: 0.8484 (m-40) cc_final: 0.8143 (t0) REVERT: A 122 ASN cc_start: 0.9123 (t0) cc_final: 0.8835 (t0) REVERT: A 222 ASN cc_start: 0.7861 (t0) cc_final: 0.7568 (t0) REVERT: A 225 ASN cc_start: 0.8403 (p0) cc_final: 0.8120 (p0) REVERT: A 232 LYS cc_start: 0.8798 (tppp) cc_final: 0.8437 (tppp) REVERT: A 256 GLU cc_start: 0.8556 (tp30) cc_final: 0.8288 (tp30) REVERT: A 257 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7305 (mm-30) REVERT: A 297 ASP cc_start: 0.8425 (p0) cc_final: 0.8191 (p0) REVERT: A 346 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8460 (mm-30) REVERT: H 60 TYR cc_start: 0.8174 (m-10) cc_final: 0.7949 (m-10) REVERT: H 85 GLN cc_start: 0.8298 (tp40) cc_final: 0.8073 (mm110) REVERT: L 37 TYR cc_start: 0.9041 (m-80) cc_final: 0.8687 (m-80) REVERT: L 83 ASP cc_start: 0.8322 (m-30) cc_final: 0.8120 (m-30) REVERT: B 63 VAL cc_start: 0.8135 (OUTLIER) cc_final: 0.7683 (p) REVERT: B 75 LYS cc_start: 0.8711 (ttmm) cc_final: 0.8312 (tttt) REVERT: B 77 THR cc_start: 0.8308 (p) cc_final: 0.8081 (p) REVERT: B 81 GLN cc_start: 0.7563 (tp40) cc_final: 0.7043 (tp40) REVERT: B 82 MET cc_start: 0.8219 (mmt) cc_final: 0.7712 (mmt) REVERT: B 83 ASN cc_start: 0.8577 (m-40) cc_final: 0.8164 (m110) outliers start: 31 outliers final: 25 residues processed: 253 average time/residue: 0.0672 time to fit residues: 23.5554 Evaluate side-chains 261 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 234 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 179 ASN Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 304 TRP Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain R residue 394 LEU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 90 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 77 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 46 ASN A 222 ASN H 80 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.086421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.075793 restraints weight = 20455.964| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.00 r_work: 0.3059 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 7882 Z= 0.279 Angle : 0.747 9.800 10776 Z= 0.381 Chirality : 0.044 0.188 1261 Planarity : 0.004 0.042 1356 Dihedral : 5.571 60.320 1137 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 4.55 % Allowed : 23.26 % Favored : 72.19 % 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 (0.27), residues: 1005 helix: 1.02 (0.30), residues: 280 sheet: -0.00 (0.30), residues: 317 loop : -0.95 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 67 TYR 0.025 0.002 TYR G 13 PHE 0.028 0.002 PHE G 6 TRP 0.016 0.002 TRP B 104 HIS 0.007 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.28 ( 7879) covalent geometry : angle 0.74481 / 0.38 (10770) SS BOND : bond 0.00144 / 0.07 ( 3) SS BOND : angle 2.44709 / 1.45 ( 6) hydrogen bonds : bond 0.04588 / 3.25 ( 347) hydrogen bonds : angle 5.43787 / 3.96 ( 984) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 232 time to evaluate : 0.311 Fit side-chains REVERT: R 131 GLN cc_start: 0.7312 (mp10) cc_final: 0.6775 (mp10) REVERT: R 141 PHE cc_start: 0.8101 (m-80) cc_final: 0.7419 (m-80) REVERT: R 304 TRP cc_start: 0.8651 (OUTLIER) cc_final: 0.7940 (m-10) REVERT: R 419 ARG cc_start: 0.8496 (ttt90) cc_final: 0.8170 (tpt170) REVERT: A 76 ARG cc_start: 0.8192 (ptm-80) cc_final: 0.7879 (ptm160) REVERT: A 122 ASN cc_start: 0.9190 (t0) cc_final: 0.8896 (t0) REVERT: A 169 GLU cc_start: 0.8265 (pm20) cc_final: 0.7923 (pm20) REVERT: A 185 GLU cc_start: 0.7227 (tp30) cc_final: 0.6869 (tp30) REVERT: A 200 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7037 (mm-30) REVERT: A 222 ASN cc_start: 0.8069 (t0) cc_final: 0.7282 (t0) REVERT: A 225 ASN cc_start: 0.8795 (p0) cc_final: 0.8552 (p0) REVERT: A 232 LYS cc_start: 0.8858 (tppp) cc_final: 0.8510 (mmmm) REVERT: A 256 GLU cc_start: 0.8615 (tp30) cc_final: 0.8323 (tp30) REVERT: A 257 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7468 (mm-30) REVERT: H 60 TYR cc_start: 0.8256 (m-10) cc_final: 0.8024 (m-10) REVERT: H 80 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8325 (t0) REVERT: H 89 LEU cc_start: 0.8920 (mm) cc_final: 0.8645 (mm) REVERT: L 30 VAL cc_start: 0.9028 (t) cc_final: 0.8825 (m) REVERT: L 37 TYR cc_start: 0.9110 (m-80) cc_final: 0.8782 (m-80) REVERT: L 83 ASP cc_start: 0.8390 (m-30) cc_final: 0.8182 (m-30) REVERT: L 91 GLN cc_start: 0.9174 (pp30) cc_final: 0.8663 (pp30) REVERT: B 63 VAL cc_start: 0.8457 (OUTLIER) cc_final: 0.8033 (p) REVERT: B 82 MET cc_start: 0.8194 (mmt) cc_final: 0.7893 (mmt) REVERT: B 83 ASN cc_start: 0.8744 (m-40) cc_final: 0.8330 (m-40) outliers start: 34 outliers final: 28 residues processed: 249 average time/residue: 0.0715 time to fit residues: 24.6174 Evaluate side-chains 255 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 224 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 179 ASN Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 304 TRP Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain R residue 394 LEU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 424 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 368 HIS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 80 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 111 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 51.3309 > 50:) chunk 22 optimal weight: 0.7980 chunk 62 optimal weight: 0.0000 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 16 optimal weight: 0.0270 chunk 32 optimal weight: 1.9990 overall best weight: 0.5042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 298 ASN H 80 ASN H 85 GLN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.090009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.079469 restraints weight = 20479.335| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.00 r_work: 0.3140 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7882 Z= 0.134 Angle : 0.699 11.745 10776 Z= 0.345 Chirality : 0.041 0.189 1261 Planarity : 0.004 0.043 1356 Dihedral : 5.224 60.361 1137 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.68 % Allowed : 23.66 % Favored : 71.66 % 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: -0.15 (0.27), residues: 1005 helix: 1.24 (0.31), residues: 278 sheet: -0.12 (0.30), residues: 315 loop : -0.94 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 22 TYR 0.016 0.001 TYR R 239 PHE 0.027 0.002 PHE G 6 TRP 0.022 0.001 TRP R 304 HIS 0.006 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 7879) covalent geometry : angle 0.69800 / 0.34 (10770) SS BOND : bond 0.00146 / 0.07 ( 3) SS BOND : angle 1.55014 / 0.89 ( 6) hydrogen bonds : bond 0.03939 / 2.76 ( 347) hydrogen bonds : angle 5.15674 / 3.70 ( 984) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 249 time to evaluate : 0.208 Fit side-chains REVERT: R 131 GLN cc_start: 0.7284 (mp10) cc_final: 0.6807 (mp10) REVERT: R 141 PHE cc_start: 0.8005 (m-80) cc_final: 0.7300 (m-80) REVERT: R 304 TRP cc_start: 0.8457 (OUTLIER) cc_final: 0.7959 (m-10) REVERT: R 352 LEU cc_start: 0.8901 (mm) cc_final: 0.8576 (mm) REVERT: R 419 ARG cc_start: 0.8466 (ttt90) cc_final: 0.8200 (tpt170) REVERT: A 76 ARG cc_start: 0.8048 (ptm-80) cc_final: 0.7773 (ptm160) REVERT: A 122 ASN cc_start: 0.9145 (t0) cc_final: 0.8868 (t0) REVERT: A 169 GLU cc_start: 0.8085 (pm20) cc_final: 0.7707 (pm20) REVERT: A 222 ASN cc_start: 0.8085 (t0) cc_final: 0.7250 (t0) REVERT: A 225 ASN cc_start: 0.8618 (p0) cc_final: 0.8395 (p0) REVERT: A 232 LYS cc_start: 0.8841 (tppp) cc_final: 0.8433 (tppp) REVERT: A 256 GLU cc_start: 0.8547 (tp30) cc_final: 0.8280 (tp30) REVERT: A 257 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7312 (mm-30) REVERT: A 297 ASP cc_start: 0.8464 (p0) cc_final: 0.8262 (p0) REVERT: H 89 LEU cc_start: 0.8776 (mm) cc_final: 0.8514 (mm) REVERT: L 37 TYR cc_start: 0.9038 (m-80) cc_final: 0.8732 (m-80) REVERT: L 83 ASP cc_start: 0.8388 (m-30) cc_final: 0.8181 (m-30) REVERT: B 63 VAL cc_start: 0.8286 (OUTLIER) cc_final: 0.7804 (p) REVERT: B 77 THR cc_start: 0.8217 (p) cc_final: 0.8002 (p) REVERT: B 83 ASN cc_start: 0.8608 (m-40) cc_final: 0.8177 (m110) outliers start: 35 outliers final: 22 residues processed: 264 average time/residue: 0.0745 time to fit residues: 27.0372 Evaluate side-chains 247 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 179 ASN Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 304 TRP Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain R residue 424 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 368 HIS Chi-restraints excluded: chain H residue 80 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 111 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 43 optimal weight: 0.0270 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.089777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.079206 restraints weight = 20416.337| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.00 r_work: 0.3130 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7882 Z= 0.148 Angle : 0.718 11.839 10776 Z= 0.352 Chirality : 0.042 0.184 1261 Planarity : 0.004 0.041 1356 Dihedral : 5.223 60.269 1137 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.74 % Allowed : 26.07 % Favored : 70.19 % 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: -0.01 (0.27), residues: 1005 helix: 1.34 (0.31), residues: 276 sheet: -0.03 (0.30), residues: 320 loop : -0.84 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 67 TYR 0.011 0.001 TYR R 233 PHE 0.028 0.002 PHE G 6 TRP 0.023 0.001 TRP R 304 HIS 0.006 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 7879) covalent geometry : angle 0.71698 / 0.35 (10770) SS BOND : bond 0.00072 / 0.04 ( 3) SS BOND : angle 1.76826 / 1.02 ( 6) hydrogen bonds : bond 0.03980 / 2.80 ( 347) hydrogen bonds : angle 5.13522 / 3.68 ( 984) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 0.272 Fit side-chains REVERT: R 141 PHE cc_start: 0.8056 (m-80) cc_final: 0.7413 (m-80) REVERT: R 304 TRP cc_start: 0.8509 (OUTLIER) cc_final: 0.8100 (m-10) REVERT: R 352 LEU cc_start: 0.8862 (mm) cc_final: 0.8512 (mm) REVERT: R 419 ARG cc_start: 0.8475 (ttt90) cc_final: 0.8199 (tpt170) REVERT: A 76 ARG cc_start: 0.8079 (ptm-80) cc_final: 0.7794 (ptm160) REVERT: A 122 ASN cc_start: 0.9136 (t0) cc_final: 0.8877 (t0) REVERT: A 169 GLU cc_start: 0.8097 (pm20) cc_final: 0.7770 (pm20) REVERT: A 222 ASN cc_start: 0.8134 (t0) cc_final: 0.7379 (t0) REVERT: A 225 ASN cc_start: 0.8644 (p0) cc_final: 0.8420 (p0) REVERT: A 232 LYS cc_start: 0.8833 (tppp) cc_final: 0.8427 (tppp) REVERT: A 256 GLU cc_start: 0.8554 (tp30) cc_final: 0.8294 (tp30) REVERT: A 257 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7325 (mm-30) REVERT: H 90 ARG cc_start: 0.8579 (ptp-110) cc_final: 0.8350 (ptp-110) REVERT: L 37 TYR cc_start: 0.9036 (m-80) cc_final: 0.8740 (m-80) REVERT: L 83 ASP cc_start: 0.8424 (m-30) cc_final: 0.8217 (m-30) REVERT: B 19 ARG cc_start: 0.7862 (tpp-160) cc_final: 0.7510 (tpt-90) REVERT: B 63 VAL cc_start: 0.8366 (OUTLIER) cc_final: 0.7900 (p) REVERT: B 77 THR cc_start: 0.8241 (p) cc_final: 0.8010 (p) REVERT: B 83 ASN cc_start: 0.8687 (m-40) cc_final: 0.8338 (m110) outliers start: 28 outliers final: 23 residues processed: 241 average time/residue: 0.0656 time to fit residues: 22.0095 Evaluate side-chains 249 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 224 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 179 ASN Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 304 TRP Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain R residue 424 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 368 HIS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 68 optimal weight: 0.0970 chunk 93 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 ASN H 80 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.090224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.079518 restraints weight = 20495.111| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.07 r_work: 0.3135 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7882 Z= 0.141 Angle : 0.733 12.162 10776 Z= 0.358 Chirality : 0.042 0.184 1261 Planarity : 0.004 0.041 1356 Dihedral : 5.204 60.214 1137 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.61 % Allowed : 26.47 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.06 (0.27), residues: 1005 helix: 1.27 (0.31), residues: 277 sheet: -0.02 (0.30), residues: 310 loop : -0.89 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 225 TYR 0.011 0.001 TYR L 92 PHE 0.029 0.002 PHE G 6 TRP 0.023 0.001 TRP R 304 HIS 0.005 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 7879) covalent geometry : angle 0.73274 / 0.36 (10770) SS BOND : bond 0.00133 / 0.07 ( 3) SS BOND : angle 1.57745 / 0.91 ( 6) hydrogen bonds : bond 0.03870 / 2.73 ( 347) hydrogen bonds : angle 5.05239 / 3.62 ( 984) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 225 time to evaluate : 0.181 Fit side-chains REVERT: R 141 PHE cc_start: 0.8070 (m-80) cc_final: 0.7410 (m-80) REVERT: R 225 ARG cc_start: 0.7423 (mtm-85) cc_final: 0.6421 (mpt180) REVERT: R 229 VAL cc_start: 0.8981 (t) cc_final: 0.8729 (p) REVERT: R 253 LEU cc_start: 0.8714 (tp) cc_final: 0.8477 (tp) REVERT: R 304 TRP cc_start: 0.8447 (OUTLIER) cc_final: 0.8052 (m-10) REVERT: R 352 LEU cc_start: 0.8863 (mm) cc_final: 0.8558 (mm) REVERT: R 419 ARG cc_start: 0.8497 (ttt90) cc_final: 0.8213 (tpt170) REVERT: A 76 ARG cc_start: 0.8087 (ptm-80) cc_final: 0.7794 (ptm160) REVERT: A 122 ASN cc_start: 0.9137 (t0) cc_final: 0.8873 (t0) REVERT: A 169 GLU cc_start: 0.8088 (pm20) cc_final: 0.7762 (pm20) REVERT: A 222 ASN cc_start: 0.8160 (t0) cc_final: 0.7398 (t0) REVERT: A 225 ASN cc_start: 0.8655 (p0) cc_final: 0.8429 (p0) REVERT: A 256 GLU cc_start: 0.8555 (tp30) cc_final: 0.8306 (tp30) REVERT: A 257 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7395 (mm-30) REVERT: H 90 ARG cc_start: 0.8618 (ptp-110) cc_final: 0.8153 (ptp-170) REVERT: L 30 VAL cc_start: 0.8972 (t) cc_final: 0.8699 (m) REVERT: L 37 TYR cc_start: 0.9030 (m-80) cc_final: 0.8728 (m-80) REVERT: L 83 ASP cc_start: 0.8427 (m-30) cc_final: 0.8223 (m-30) REVERT: B 63 VAL cc_start: 0.8408 (OUTLIER) cc_final: 0.7933 (p) REVERT: B 77 THR cc_start: 0.8232 (p) cc_final: 0.8008 (p) REVERT: B 83 ASN cc_start: 0.8692 (m-40) cc_final: 0.8347 (m-40) outliers start: 27 outliers final: 22 residues processed: 237 average time/residue: 0.0659 time to fit residues: 21.4900 Evaluate side-chains 244 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 179 ASN Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 304 TRP Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain R residue 424 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 368 HIS Chi-restraints excluded: chain H residue 80 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 39 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 67 optimal weight: 0.1980 chunk 38 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 80 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.090139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.079584 restraints weight = 20398.113| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.99 r_work: 0.3139 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7882 Z= 0.146 Angle : 0.742 11.836 10776 Z= 0.360 Chirality : 0.042 0.178 1261 Planarity : 0.004 0.041 1356 Dihedral : 5.208 60.032 1137 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.88 % Allowed : 26.47 % Favored : 69.65 % 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: -0.11 (0.27), residues: 1005 helix: 1.36 (0.31), residues: 274 sheet: -0.11 (0.30), residues: 306 loop : -0.94 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.012 0.001 TYR R 233 PHE 0.029 0.002 PHE G 6 TRP 0.022 0.001 TRP R 304 HIS 0.005 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 7879) covalent geometry : angle 0.74166 / 0.36 (10770) SS BOND : bond 0.00113 / 0.06 ( 3) SS BOND : angle 1.57893 / 0.91 ( 6) hydrogen bonds : bond 0.03871 / 2.72 ( 347) hydrogen bonds : angle 5.02432 / 3.59 ( 984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1711.95 seconds wall clock time: 29 minutes 59.24 seconds (1799.24 seconds total)