Starting phenix.real_space_refine on Wed Sep 17 17:08:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e90_47738/09_2025/9e90_47738.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e90_47738/09_2025/9e90_47738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e90_47738/09_2025/9e90_47738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e90_47738/09_2025/9e90_47738.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e90_47738/09_2025/9e90_47738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e90_47738/09_2025/9e90_47738.map" } resolution = 3.45 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= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 6 5.49 5 S 28 5.16 5 C 6103 2.51 5 N 1675 2.21 5 O 1859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9672 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2109 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain: "A" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3731 Classifications: {'peptide': 483} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 17, 'TRANS': 465} Chain breaks: 2 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 9, 'GLN:plan1': 2, 'ARG:plan': 1, 'PHE:plan': 3, 'TYR:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 101 Chain: "C" Number of atoms: 3769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3769 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 17, 'TRANS': 463} Chain breaks: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 5, 'ASP:plan': 4, 'PHE:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 63 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 467 SG CYS B 57 40.233 61.353 33.829 1.00 65.56 S ATOM 798 SG CYS B 98 39.157 65.237 34.684 1.00 64.46 S ATOM 924 SG CYS B 116 41.803 63.700 32.700 1.00 66.41 S Time building chain proxies: 2.43, per 1000 atoms: 0.25 Number of scatterers: 9672 At special positions: 0 Unit cell: (94.83, 134.07, 120.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 28 16.00 P 6 15.00 O 1859 8.00 N 1675 7.00 C 6103 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 377.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 116 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 98 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 57 " 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2308 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 12 sheets defined 47.6% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'B' and resid 14 through 21 removed outlier: 3.921A pdb=" N PHE B 18 " --> pdb=" O PHE B 14 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 19 " --> pdb=" O LEU B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 32 Processing helix chain 'B' and resid 36 through 50 removed outlier: 3.607A pdb=" N ASP B 49 " --> pdb=" O HIS B 45 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 69 removed outlier: 3.612A pdb=" N GLU B 68 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 80 removed outlier: 3.895A pdb=" N SER B 80 " --> pdb=" O LYS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 127 removed outlier: 3.810A pdb=" N SER B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 178 No H-bonds generated for 'chain 'B' and resid 176 through 178' Processing helix chain 'B' and resid 179 through 192 removed outlier: 3.963A pdb=" N ILE B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 191 " --> pdb=" O THR B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 202 through 212 removed outlier: 3.944A pdb=" N LEU B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 229 removed outlier: 3.674A pdb=" N LEU B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'A' and resid 8 through 17 Processing helix chain 'A' and resid 21 through 26 removed outlier: 3.845A pdb=" N GLN A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 32 Processing helix chain 'A' and resid 43 through 48 removed outlier: 4.361A pdb=" N TYR A 47 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 48 " --> pdb=" O MET A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 48' Processing helix chain 'A' and resid 98 through 118 removed outlier: 3.853A pdb=" N LEU A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N HIS A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 187 Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 224 through 230 removed outlier: 3.502A pdb=" N ALA A 228 " --> pdb=" O LYS A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 261 removed outlier: 3.557A pdb=" N THR A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 332 removed outlier: 3.963A pdb=" N PHE A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 361 No H-bonds generated for 'chain 'A' and resid 359 through 361' Processing helix chain 'A' and resid 362 through 383 Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 412 through 421 Processing helix chain 'A' and resid 432 through 437 removed outlier: 3.763A pdb=" N CYS A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS A 437 " --> pdb=" O PRO A 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 432 through 437' Processing helix chain 'A' and resid 438 through 439 No H-bonds generated for 'chain 'A' and resid 438 through 439' Processing helix chain 'A' and resid 440 through 443 Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 484 through 495 removed outlier: 3.523A pdb=" N LEU A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 516 removed outlier: 3.507A pdb=" N HIS A 514 " --> pdb=" O THR A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 542 removed outlier: 3.549A pdb=" N GLN A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 19 removed outlier: 3.579A pdb=" N THR C 10 " --> pdb=" O PRO C 6 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LYS C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 31 removed outlier: 4.018A pdb=" N SER C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS C 29 " --> pdb=" O TYR C 25 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL C 30 " --> pdb=" O GLN C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 54 removed outlier: 3.613A pdb=" N ASP C 46 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.003A pdb=" N HIS C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 112 " --> pdb=" O GLY C 108 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 131 Processing helix chain 'C' and resid 171 through 187 removed outlier: 3.800A pdb=" N GLU C 175 " --> pdb=" O SER C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.762A pdb=" N ALA C 228 " --> pdb=" O LYS C 225 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR C 229 " --> pdb=" O PHE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 254 removed outlier: 3.930A pdb=" N ASN C 254 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 332 removed outlier: 3.695A pdb=" N LEU C 321 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N HIS C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 383 removed outlier: 3.666A pdb=" N ILE C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 421 Processing helix chain 'C' and resid 432 through 437 Processing helix chain 'C' and resid 438 through 439 No H-bonds generated for 'chain 'C' and resid 438 through 439' Processing helix chain 'C' and resid 440 through 442 No H-bonds generated for 'chain 'C' and resid 440 through 442' Processing helix chain 'C' and resid 463 through 472 Processing helix chain 'C' and resid 481 through 495 removed outlier: 3.627A pdb=" N PHE C 495 " --> pdb=" O LYS C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 516 removed outlier: 3.905A pdb=" N LEU C 507 " --> pdb=" O ASP C 503 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS C 514 " --> pdb=" O THR C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 539 removed outlier: 3.857A pdb=" N ASP C 537 " --> pdb=" O ILE C 533 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE C 538 " --> pdb=" O TRP C 534 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 70 through 73 Processing sheet with id=AA2, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 80 removed outlier: 3.572A pdb=" N LEU A 77 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP A 65 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN A 143 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 77 through 80 removed outlier: 3.572A pdb=" N LEU A 77 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP A 65 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN A 143 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 138 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 157 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 91 through 92 removed outlier: 6.826A pdb=" N VAL A 91 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 197 through 198 Processing sheet with id=AA7, first strand: chain 'A' and resid 335 through 341 removed outlier: 5.063A pdb=" N ASN A 337 " --> pdb=" O ASP A 350 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP A 350 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 346 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 80 removed outlier: 3.588A pdb=" N LEU C 68 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 66 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N VAL C 63 " --> pdb=" O ASP C 145 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP C 145 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP C 65 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU C 69 " --> pdb=" O SER C 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 80 removed outlier: 3.588A pdb=" N LEU C 68 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 66 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N VAL C 63 " --> pdb=" O ASP C 145 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP C 145 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP C 65 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU C 69 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR C 157 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 428 through 429 removed outlier: 6.816A pdb=" N ILE C 89 " --> pdb=" O TRP C 445 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 194 through 198 Processing sheet with id=AB3, first strand: chain 'C' and resid 335 through 341 removed outlier: 5.383A pdb=" N ASN C 337 " --> pdb=" O ASP C 350 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP C 350 " --> pdb=" O ASN C 337 " (cutoff:3.500A) 393 hydrogen bonds defined for protein. 1131 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: 1.64 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3205 1.34 - 1.46: 2007 1.46 - 1.58: 4593 1.58 - 1.70: 14 1.70 - 1.82: 43 Bond restraints: 9862 Sorted by residual: bond pdb=" C2' ATP A 602 " pdb=" C3' ATP A 602 " ideal model delta sigma weight residual 1.531 1.260 0.271 1.20e-02 6.94e+03 5.09e+02 bond pdb=" C2' ATP A 601 " pdb=" C3' ATP A 601 " ideal model delta sigma weight residual 1.531 1.265 0.266 1.20e-02 6.94e+03 4.92e+02 bond pdb=" C6 ATP A 601 " pdb=" N6 ATP A 601 " ideal model delta sigma weight residual 1.337 1.480 -0.143 1.10e-02 8.26e+03 1.70e+02 bond pdb=" C6 ATP A 602 " pdb=" N6 ATP A 602 " ideal model delta sigma weight residual 1.337 1.480 -0.143 1.10e-02 8.26e+03 1.68e+02 bond pdb=" C1' ATP A 602 " pdb=" C2' ATP A 602 " ideal model delta sigma weight residual 1.531 1.659 -0.128 1.20e-02 6.94e+03 1.14e+02 ... (remaining 9857 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 13245 3.18 - 6.35: 85 6.35 - 9.53: 17 9.53 - 12.71: 1 12.71 - 15.88: 4 Bond angle restraints: 13352 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 123.99 15.88 1.00e+00 1.00e+00 2.52e+02 angle pdb=" PB ATP A 602 " pdb=" O3B ATP A 602 " pdb=" PG ATP A 602 " ideal model delta sigma weight residual 139.87 123.99 15.88 1.00e+00 1.00e+00 2.52e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 124.10 12.73 1.00e+00 1.00e+00 1.62e+02 angle pdb=" PA ATP A 602 " pdb=" O3A ATP A 602 " pdb=" PB ATP A 602 " ideal model delta sigma weight residual 136.83 124.12 12.71 1.00e+00 1.00e+00 1.62e+02 angle pdb=" C5 ATP A 602 " pdb=" C4 ATP A 602 " pdb=" N3 ATP A 602 " ideal model delta sigma weight residual 126.80 119.07 7.73 1.00e+00 1.00e+00 5.97e+01 ... (remaining 13347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 5498 17.58 - 35.15: 407 35.15 - 52.73: 47 52.73 - 70.31: 41 70.31 - 87.88: 4 Dihedral angle restraints: 5997 sinusoidal: 2438 harmonic: 3559 Sorted by residual: dihedral pdb=" CA PRO A 344 " pdb=" C PRO A 344 " pdb=" N LEU A 345 " pdb=" CA LEU A 345 " ideal model delta harmonic sigma weight residual 180.00 -152.57 -27.43 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA ALA A 343 " pdb=" C ALA A 343 " pdb=" N PRO A 344 " pdb=" CA PRO A 344 " ideal model delta harmonic sigma weight residual -180.00 -158.14 -21.86 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ASP C 145 " pdb=" C ASP C 145 " pdb=" N TYR C 146 " pdb=" CA TYR C 146 " ideal model delta harmonic sigma weight residual 180.00 160.45 19.55 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 5994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1198 0.053 - 0.106: 239 0.106 - 0.159: 42 0.159 - 0.212: 5 0.212 - 0.265: 4 Chirality restraints: 1488 Sorted by residual: chirality pdb=" C3' ATP A 601 " pdb=" C2' ATP A 601 " pdb=" C4' ATP A 601 " pdb=" O3' ATP A 601 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C2' ATP A 601 " pdb=" C1' ATP A 601 " pdb=" C3' ATP A 601 " pdb=" O2' ATP A 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.42 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C3' ATP A 602 " pdb=" C2' ATP A 602 " pdb=" C4' ATP A 602 " pdb=" O3' ATP A 602 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 1485 not shown) Planarity restraints: 1718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 246 " -0.024 2.00e-02 2.50e+03 1.78e-02 5.54e+00 pdb=" CG PHE C 246 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE C 246 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE C 246 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 246 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 246 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 246 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 406 " -0.038 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO A 407 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 407 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 407 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 89 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" C ILE A 89 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE A 89 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU A 90 " -0.012 2.00e-02 2.50e+03 ... (remaining 1715 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 79 2.64 - 3.21: 9026 3.21 - 3.77: 13994 3.77 - 4.34: 19549 4.34 - 4.90: 32246 Nonbonded interactions: 74894 Sorted by model distance: nonbonded pdb=" OG SER C 16 " pdb=" OG SER C 24 " model vdw 2.076 3.040 nonbonded pdb=" O PRO A 188 " pdb=" NZ LYS A 225 " model vdw 2.113 3.120 nonbonded pdb=" O PRO C 193 " pdb=" OH TYR C 229 " model vdw 2.143 3.040 nonbonded pdb=" OG1 THR B 102 " pdb=" OE2 GLU B 109 " model vdw 2.183 3.040 nonbonded pdb=" NH1 ARG B 5 " pdb=" OD1 ASN B 7 " model vdw 2.265 3.120 ... (remaining 74889 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 1 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 11 or (resid 12 through 15 and (name N or name CA \ or name C or name O or name CB )) or resid 16 through 19 or (resid 20 through 2 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 23 through 2 \ 5 or (resid 26 through 31 and (name N or name CA or name C or name O or name CB \ )) or resid 32 through 237 or (resid 238 and (name N or name CA or name C or nam \ e O or name CB )) or resid 239 through 254 or resid 316 through 345 or (resid 34 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 347 through \ 540)) selection = (chain 'C' and ((resid 1 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 8 or (resid 9 and (name N or name CA or name C or \ name O or name CB )) or resid 10 through 12 or (resid 13 through 15 and (name N \ or name CA or name C or name O or name CB )) or resid 16 through 27 or (resid 2 \ 8 through 31 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 2 or (resid 33 through 36 and (name N or name CA or name C or name O or name CB \ )) or resid 37 or (resid 38 through 39 and (name N or name CA or name C or name \ O or name CB )) or resid 40 through 43 or (resid 44 and (name N or name CA or na \ me C or name O or name CB )) or resid 45 or (resid 46 through 50 and (name N or \ name CA or name C or name O or name CB )) or resid 51 or resid 57 through 59 or \ (resid 60 and (name N or name CA or name C or name O or name CB )) or resid 61 t \ hrough 129 or (resid 130 and (name N or name CA or name C or name O or name CB ) \ ) or resid 131 through 214 or (resid 215 through 216 and (name N or name CA or n \ ame C or name O or name CB )) or resid 217 or (resid 218 and (name N or name CA \ or name C or name O or name CB )) or resid 219 through 254 or resid 316 through \ 540)) } 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: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.540 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.271 9867 Z= 0.523 Angle : 0.748 15.882 13352 Z= 0.473 Chirality : 0.046 0.265 1488 Planarity : 0.005 0.057 1718 Dihedral : 13.389 87.884 3689 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.65 % Favored : 88.10 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 aren not related in a simple way. whole: -1.68 (0.24), residues: 1210 helix: 0.29 (0.23), residues: 503 sheet: -1.94 (0.42), residues: 130 loop : -2.24 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 378 TYR 0.021 0.002 TYR B 119 PHE 0.038 0.002 PHE C 246 TRP 0.023 0.002 TRP B 27 HIS 0.005 0.001 HIS C 437 Details of bonding type rmsd covalent geometry : bond 0.00680 ( 9862) covalent geometry : angle 0.74775 (13352) hydrogen bonds : bond 0.17462 ( 380) hydrogen bonds : angle 6.71222 ( 1131) metal coordination : bond 0.00126 ( 3) Misc. bond : bond 0.00092 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 ASP cc_start: 0.6499 (t0) cc_final: 0.6058 (t0) REVERT: B 208 HIS cc_start: 0.7145 (t70) cc_final: 0.6929 (t-90) REVERT: A 115 ARG cc_start: 0.7985 (mtt90) cc_final: 0.7651 (mtt-85) REVERT: A 200 VAL cc_start: 0.7990 (m) cc_final: 0.7689 (p) REVERT: A 243 PHE cc_start: 0.6850 (t80) cc_final: 0.6597 (t80) REVERT: A 393 THR cc_start: 0.7606 (t) cc_final: 0.7253 (m) REVERT: A 418 GLU cc_start: 0.7275 (tt0) cc_final: 0.7041 (tt0) REVERT: A 434 GLN cc_start: 0.7940 (mp-120) cc_final: 0.7636 (mp10) REVERT: A 469 GLU cc_start: 0.6295 (tt0) cc_final: 0.6093 (tt0) REVERT: A 528 GLU cc_start: 0.7360 (mm-30) cc_final: 0.6471 (mm-30) REVERT: A 533 ILE cc_start: 0.7718 (mt) cc_final: 0.7465 (tp) REVERT: A 534 TRP cc_start: 0.7190 (t60) cc_final: 0.6175 (t60) REVERT: A 535 GLU cc_start: 0.7478 (mm-30) cc_final: 0.5581 (mm-30) REVERT: C 1 MET cc_start: 0.7351 (mtm) cc_final: 0.6906 (ppp) REVERT: C 75 GLU cc_start: 0.7732 (tp30) cc_final: 0.7469 (tm-30) REVERT: C 76 SER cc_start: 0.8225 (t) cc_final: 0.7956 (m) REVERT: C 109 LEU cc_start: 0.7316 (mm) cc_final: 0.7096 (mt) REVERT: C 127 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7377 (mt-10) REVERT: C 146 TYR cc_start: 0.7642 (t80) cc_final: 0.7064 (t80) REVERT: C 236 LYS cc_start: 0.6819 (pttm) cc_final: 0.6608 (pttm) REVERT: C 374 ASP cc_start: 0.6472 (t0) cc_final: 0.6078 (t0) REVERT: C 398 ILE cc_start: 0.7695 (mt) cc_final: 0.7346 (mp) REVERT: C 416 ARG cc_start: 0.6228 (mtm110) cc_final: 0.5534 (mmp-170) REVERT: C 418 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7205 (mt-10) REVERT: C 448 LYS cc_start: 0.8181 (tttt) cc_final: 0.7797 (ptmm) REVERT: C 469 GLU cc_start: 0.7548 (tt0) cc_final: 0.7323 (tt0) REVERT: C 470 ASN cc_start: 0.7257 (m110) cc_final: 0.6909 (m110) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.1189 time to fit residues: 48.2164 Evaluate side-chains 248 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 HIS ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN A 411 GLN C 70 ASN C 111 HIS C 184 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.154681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.132733 restraints weight = 13535.716| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.39 r_work: 0.3684 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9867 Z= 0.178 Angle : 0.666 11.178 13352 Z= 0.343 Chirality : 0.045 0.218 1488 Planarity : 0.005 0.068 1718 Dihedral : 7.852 68.142 1369 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.99 % Favored : 88.76 % Rotamer: Outliers : 2.03 % Allowed : 9.46 % Favored : 88.51 % 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 aren not related in a simple way. whole: -1.46 (0.24), residues: 1210 helix: 0.47 (0.23), residues: 522 sheet: -1.68 (0.46), residues: 120 loop : -2.25 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 202 TYR 0.024 0.002 TYR C 71 PHE 0.015 0.002 PHE B 30 TRP 0.018 0.002 TRP C 223 HIS 0.011 0.001 HIS C 437 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 9862) covalent geometry : angle 0.66554 (13352) hydrogen bonds : bond 0.04914 ( 380) hydrogen bonds : angle 5.19849 ( 1131) metal coordination : bond 0.00614 ( 3) Misc. bond : bond 0.00281 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 257 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 ASP cc_start: 0.6855 (t0) cc_final: 0.6211 (t0) REVERT: B 135 THR cc_start: 0.8347 (m) cc_final: 0.8042 (m) REVERT: B 229 ASN cc_start: 0.7997 (t0) cc_final: 0.7514 (t0) REVERT: A 115 ARG cc_start: 0.8153 (mtt90) cc_final: 0.7757 (mtt-85) REVERT: A 191 SER cc_start: 0.8407 (m) cc_final: 0.7879 (p) REVERT: A 230 ASN cc_start: 0.7714 (m110) cc_final: 0.7502 (m110) REVERT: A 243 PHE cc_start: 0.7152 (t80) cc_final: 0.6837 (t80) REVERT: A 393 THR cc_start: 0.7910 (t) cc_final: 0.7586 (m) REVERT: A 533 ILE cc_start: 0.7716 (mt) cc_final: 0.7516 (tp) REVERT: A 534 TRP cc_start: 0.7096 (t60) cc_final: 0.6046 (t60) REVERT: C 1 MET cc_start: 0.7457 (mtm) cc_final: 0.6916 (ppp) REVERT: C 76 SER cc_start: 0.8459 (t) cc_final: 0.8247 (m) REVERT: C 109 LEU cc_start: 0.7495 (mm) cc_final: 0.7166 (mt) REVERT: C 182 THR cc_start: 0.8306 (m) cc_final: 0.8041 (p) REVERT: C 398 ILE cc_start: 0.8076 (mt) cc_final: 0.7625 (mt) REVERT: C 402 ASP cc_start: 0.6988 (p0) cc_final: 0.6779 (p0) REVERT: C 416 ARG cc_start: 0.6674 (mtm110) cc_final: 0.5903 (mmp-170) REVERT: C 448 LYS cc_start: 0.8367 (tttt) cc_final: 0.7868 (ptmm) REVERT: C 468 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7557 (tp) REVERT: C 469 GLU cc_start: 0.7978 (tt0) cc_final: 0.7765 (tt0) REVERT: C 470 ASN cc_start: 0.7640 (m110) cc_final: 0.7155 (m110) outliers start: 21 outliers final: 12 residues processed: 262 average time/residue: 0.1068 time to fit residues: 37.4040 Evaluate side-chains 248 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 235 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 385 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 468 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 85 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS A 86 ASN A 111 HIS A 184 HIS A 411 GLN ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.148799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.126666 restraints weight = 13684.657| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.38 r_work: 0.3588 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 9867 Z= 0.285 Angle : 0.738 11.252 13352 Z= 0.383 Chirality : 0.048 0.160 1488 Planarity : 0.005 0.065 1718 Dihedral : 8.220 74.795 1369 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.74 % Favored : 88.10 % Rotamer: Outliers : 3.38 % Allowed : 11.20 % Favored : 85.42 % 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 aren not related in a simple way. whole: -1.76 (0.24), residues: 1210 helix: 0.23 (0.22), residues: 526 sheet: -2.00 (0.44), residues: 130 loop : -2.39 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 202 TYR 0.031 0.002 TYR C 71 PHE 0.023 0.003 PHE C 192 TRP 0.025 0.002 TRP C 223 HIS 0.012 0.002 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00655 ( 9862) covalent geometry : angle 0.73776 (13352) hydrogen bonds : bond 0.05434 ( 380) hydrogen bonds : angle 5.23711 ( 1131) metal coordination : bond 0.01979 ( 3) Misc. bond : bond 0.00266 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 246 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 LEU cc_start: 0.7521 (mt) cc_final: 0.7285 (mp) REVERT: B 133 ASP cc_start: 0.6946 (t0) cc_final: 0.6335 (t0) REVERT: B 135 THR cc_start: 0.8444 (m) cc_final: 0.8169 (m) REVERT: B 229 ASN cc_start: 0.8196 (t0) cc_final: 0.7715 (t0) REVERT: B 234 LYS cc_start: 0.7477 (mmtt) cc_final: 0.7258 (mmtp) REVERT: A 71 TYR cc_start: 0.7833 (t80) cc_final: 0.7216 (t80) REVERT: A 86 ASN cc_start: 0.8074 (OUTLIER) cc_final: 0.6445 (p0) REVERT: A 115 ARG cc_start: 0.8195 (mtt90) cc_final: 0.7956 (mtt-85) REVERT: A 162 TYR cc_start: 0.6637 (m-10) cc_final: 0.6395 (m-10) REVERT: A 164 ASP cc_start: 0.7536 (p0) cc_final: 0.6757 (m-30) REVERT: A 191 SER cc_start: 0.8595 (m) cc_final: 0.8149 (p) REVERT: A 230 ASN cc_start: 0.7861 (m110) cc_final: 0.7486 (m110) REVERT: A 243 PHE cc_start: 0.7418 (t80) cc_final: 0.6975 (t80) REVERT: A 374 ASP cc_start: 0.7307 (t0) cc_final: 0.6805 (t0) REVERT: A 393 THR cc_start: 0.8222 (t) cc_final: 0.7907 (m) REVERT: A 418 GLU cc_start: 0.7746 (tt0) cc_final: 0.7466 (mt-10) REVERT: A 533 ILE cc_start: 0.7758 (mt) cc_final: 0.7550 (tp) REVERT: C 1 MET cc_start: 0.7261 (mtm) cc_final: 0.6691 (ppp) REVERT: C 74 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.6942 (m-10) REVERT: C 76 SER cc_start: 0.8593 (t) cc_final: 0.8384 (m) REVERT: C 109 LEU cc_start: 0.7572 (mm) cc_final: 0.7305 (mt) REVERT: C 127 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7649 (mp0) REVERT: C 182 THR cc_start: 0.8344 (m) cc_final: 0.8053 (p) REVERT: C 398 ILE cc_start: 0.8260 (mt) cc_final: 0.7753 (mt) REVERT: C 416 ARG cc_start: 0.6773 (mtm110) cc_final: 0.5936 (mmp-170) REVERT: C 448 LYS cc_start: 0.8464 (tttt) cc_final: 0.7959 (ptmm) REVERT: C 468 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7868 (tp) REVERT: C 470 ASN cc_start: 0.7864 (m110) cc_final: 0.7423 (m110) outliers start: 35 outliers final: 23 residues processed: 261 average time/residue: 0.1020 time to fit residues: 35.7377 Evaluate side-chains 256 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 529 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 56 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 100 optimal weight: 0.2980 chunk 68 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 ASN A 470 ASN ** A 476 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 = 0.4028 r_free = 0.4028 target = 0.150907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.127351 restraints weight = 13801.547| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.48 r_work: 0.3610 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9867 Z= 0.178 Angle : 0.648 11.098 13352 Z= 0.334 Chirality : 0.044 0.169 1488 Planarity : 0.005 0.053 1718 Dihedral : 7.957 78.215 1369 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.65 % Favored : 88.10 % Rotamer: Outliers : 3.19 % Allowed : 13.90 % Favored : 82.92 % 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 aren not related in a simple way. whole: -1.54 (0.24), residues: 1210 helix: 0.43 (0.23), residues: 525 sheet: -1.62 (0.46), residues: 126 loop : -2.35 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 244 TYR 0.018 0.002 TYR C 71 PHE 0.012 0.002 PHE C 426 TRP 0.015 0.002 TRP C 466 HIS 0.010 0.001 HIS C 437 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 9862) covalent geometry : angle 0.64758 (13352) hydrogen bonds : bond 0.04478 ( 380) hydrogen bonds : angle 4.92382 ( 1131) metal coordination : bond 0.01012 ( 3) Misc. bond : bond 0.00195 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 232 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LYS cc_start: 0.7659 (mmmt) cc_final: 0.7299 (mmmt) REVERT: B 49 ASP cc_start: 0.7163 (t0) cc_final: 0.6675 (t0) REVERT: B 91 TRP cc_start: 0.8063 (t-100) cc_final: 0.7859 (t-100) REVERT: B 99 LEU cc_start: 0.7300 (mt) cc_final: 0.7075 (mp) REVERT: B 133 ASP cc_start: 0.6825 (t0) cc_final: 0.6180 (t0) REVERT: B 135 THR cc_start: 0.8381 (m) cc_final: 0.8094 (m) REVERT: B 229 ASN cc_start: 0.8018 (t0) cc_final: 0.7506 (t0) REVERT: A 71 TYR cc_start: 0.7589 (t80) cc_final: 0.7019 (t80) REVERT: A 86 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.6701 (p0) REVERT: A 191 SER cc_start: 0.8499 (m) cc_final: 0.8028 (p) REVERT: A 230 ASN cc_start: 0.7773 (m110) cc_final: 0.7369 (m110) REVERT: A 243 PHE cc_start: 0.7268 (t80) cc_final: 0.6783 (t80) REVERT: A 374 ASP cc_start: 0.7109 (t0) cc_final: 0.6814 (t0) REVERT: A 393 THR cc_start: 0.8093 (t) cc_final: 0.7720 (m) REVERT: A 418 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7340 (mt-10) REVERT: A 524 GLU cc_start: 0.7453 (tp30) cc_final: 0.7135 (mm-30) REVERT: A 535 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7267 (tp30) REVERT: C 1 MET cc_start: 0.7249 (mtm) cc_final: 0.6701 (ppp) REVERT: C 76 SER cc_start: 0.8525 (t) cc_final: 0.8275 (m) REVERT: C 109 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7238 (mt) REVERT: C 127 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7475 (mp0) REVERT: C 182 THR cc_start: 0.8258 (m) cc_final: 0.8051 (p) REVERT: C 398 ILE cc_start: 0.8158 (mt) cc_final: 0.7573 (mt) REVERT: C 416 ARG cc_start: 0.6655 (mtm110) cc_final: 0.5945 (mmp-170) REVERT: C 448 LYS cc_start: 0.8414 (tttt) cc_final: 0.7899 (ptmm) REVERT: C 468 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7775 (tp) REVERT: C 470 ASN cc_start: 0.7604 (m110) cc_final: 0.7124 (m110) outliers start: 33 outliers final: 22 residues processed: 247 average time/residue: 0.1071 time to fit residues: 35.6554 Evaluate side-chains 251 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 225 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 506 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 21 optimal weight: 0.9990 chunk 89 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 44 optimal weight: 0.2980 chunk 97 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 116 optimal weight: 0.6980 chunk 110 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.151243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.128662 restraints weight = 13646.619| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.40 r_work: 0.3624 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9867 Z= 0.169 Angle : 0.637 10.678 13352 Z= 0.327 Chirality : 0.044 0.160 1488 Planarity : 0.005 0.053 1718 Dihedral : 7.871 82.647 1369 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.99 % Favored : 88.76 % Rotamer: Outliers : 3.57 % Allowed : 15.06 % Favored : 81.37 % 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 aren not related in a simple way. whole: -1.44 (0.24), residues: 1210 helix: 0.55 (0.22), residues: 525 sheet: -1.45 (0.46), residues: 124 loop : -2.38 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 244 TYR 0.016 0.002 TYR C 71 PHE 0.012 0.002 PHE B 235 TRP 0.015 0.001 TRP B 91 HIS 0.009 0.001 HIS C 437 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 9862) covalent geometry : angle 0.63669 (13352) hydrogen bonds : bond 0.04267 ( 380) hydrogen bonds : angle 4.79676 ( 1131) metal coordination : bond 0.00989 ( 3) Misc. bond : bond 0.00180 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 228 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 ASP cc_start: 0.7134 (t0) cc_final: 0.6681 (t0) REVERT: B 99 LEU cc_start: 0.7397 (mt) cc_final: 0.7176 (mp) REVERT: B 133 ASP cc_start: 0.6775 (t0) cc_final: 0.6170 (t0) REVERT: B 135 THR cc_start: 0.8363 (m) cc_final: 0.8082 (m) REVERT: B 229 ASN cc_start: 0.7984 (t0) cc_final: 0.7450 (t0) REVERT: A 86 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.6747 (p0) REVERT: A 191 SER cc_start: 0.8496 (m) cc_final: 0.8040 (p) REVERT: A 230 ASN cc_start: 0.7798 (m110) cc_final: 0.7368 (m110) REVERT: A 243 PHE cc_start: 0.7229 (t80) cc_final: 0.6723 (t80) REVERT: A 374 ASP cc_start: 0.7161 (t0) cc_final: 0.6913 (t0) REVERT: A 393 THR cc_start: 0.8012 (t) cc_final: 0.7761 (m) REVERT: C 1 MET cc_start: 0.7245 (mtm) cc_final: 0.6720 (ppp) REVERT: C 60 GLN cc_start: 0.7893 (tt0) cc_final: 0.7667 (tt0) REVERT: C 76 SER cc_start: 0.8485 (t) cc_final: 0.8281 (m) REVERT: C 109 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7252 (mt) REVERT: C 127 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7498 (mp0) REVERT: C 163 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6786 (mp0) REVERT: C 182 THR cc_start: 0.8264 (m) cc_final: 0.8059 (p) REVERT: C 398 ILE cc_start: 0.8199 (mt) cc_final: 0.7551 (mt) REVERT: C 416 ARG cc_start: 0.6599 (mtm110) cc_final: 0.5947 (mmp-170) REVERT: C 468 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7750 (tp) REVERT: C 470 ASN cc_start: 0.7572 (m110) cc_final: 0.7079 (m110) REVERT: C 537 ASP cc_start: 0.7665 (t0) cc_final: 0.7255 (t0) outliers start: 37 outliers final: 24 residues processed: 247 average time/residue: 0.1028 time to fit residues: 34.3590 Evaluate side-chains 246 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 506 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 6 optimal weight: 0.9980 chunk 113 optimal weight: 0.0570 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 ASN A 169 ASN C 204 ASN C 388 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.150848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.128233 restraints weight = 13701.160| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.39 r_work: 0.3615 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9867 Z= 0.186 Angle : 0.666 10.532 13352 Z= 0.340 Chirality : 0.044 0.155 1488 Planarity : 0.005 0.070 1718 Dihedral : 7.954 87.872 1369 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.65 % Favored : 88.10 % Rotamer: Outliers : 3.86 % Allowed : 15.93 % 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 aren not related in a simple way. whole: -1.43 (0.24), residues: 1210 helix: 0.51 (0.22), residues: 528 sheet: -1.41 (0.46), residues: 124 loop : -2.34 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 532 TYR 0.016 0.002 TYR C 71 PHE 0.020 0.002 PHE A 335 TRP 0.018 0.002 TRP B 91 HIS 0.009 0.001 HIS C 437 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 9862) covalent geometry : angle 0.66614 (13352) hydrogen bonds : bond 0.04294 ( 380) hydrogen bonds : angle 4.76540 ( 1131) metal coordination : bond 0.01074 ( 3) Misc. bond : bond 0.00190 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 223 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 ASP cc_start: 0.7138 (t0) cc_final: 0.6639 (t0) REVERT: B 50 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6494 (mt0) REVERT: B 99 LEU cc_start: 0.7433 (mt) cc_final: 0.7162 (mp) REVERT: B 133 ASP cc_start: 0.6753 (t0) cc_final: 0.6155 (t0) REVERT: B 135 THR cc_start: 0.8385 (m) cc_final: 0.8118 (m) REVERT: B 229 ASN cc_start: 0.7982 (t0) cc_final: 0.7436 (t0) REVERT: A 86 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.6875 (p0) REVERT: A 191 SER cc_start: 0.8517 (m) cc_final: 0.8063 (p) REVERT: A 230 ASN cc_start: 0.7795 (m110) cc_final: 0.7458 (m110) REVERT: A 243 PHE cc_start: 0.7151 (t80) cc_final: 0.6742 (t80) REVERT: A 374 ASP cc_start: 0.7108 (t0) cc_final: 0.6864 (t0) REVERT: A 393 THR cc_start: 0.8050 (t) cc_final: 0.7830 (m) REVERT: A 418 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7381 (mt-10) REVERT: A 533 ILE cc_start: 0.7763 (tp) cc_final: 0.7520 (tt) REVERT: C 1 MET cc_start: 0.7231 (mtm) cc_final: 0.6766 (ppp) REVERT: C 74 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.6775 (m-10) REVERT: C 76 SER cc_start: 0.8500 (t) cc_final: 0.8296 (m) REVERT: C 109 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7267 (mt) REVERT: C 127 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7513 (mp0) REVERT: C 163 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6788 (mp0) REVERT: C 391 ASP cc_start: 0.7622 (p0) cc_final: 0.7259 (p0) REVERT: C 398 ILE cc_start: 0.8221 (mt) cc_final: 0.7545 (mt) REVERT: C 416 ARG cc_start: 0.6616 (mtm110) cc_final: 0.5989 (mmp-170) REVERT: C 468 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7757 (tp) REVERT: C 470 ASN cc_start: 0.7555 (m110) cc_final: 0.7039 (m110) REVERT: C 537 ASP cc_start: 0.7668 (t0) cc_final: 0.7258 (t0) outliers start: 40 outliers final: 27 residues processed: 245 average time/residue: 0.1106 time to fit residues: 36.5217 Evaluate side-chains 250 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 217 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 245 ARG Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 506 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 57 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 70 optimal weight: 0.6980 chunk 118 optimal weight: 0.3980 chunk 84 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 GLN A 86 ASN ** A 476 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 = 0.4029 r_free = 0.4029 target = 0.150899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.128943 restraints weight = 13750.455| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.40 r_work: 0.3611 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9867 Z= 0.187 Angle : 0.671 10.506 13352 Z= 0.343 Chirality : 0.045 0.160 1488 Planarity : 0.005 0.071 1718 Dihedral : 7.931 89.338 1369 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.49 % Favored : 88.26 % Rotamer: Outliers : 4.15 % Allowed : 16.41 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.24), residues: 1210 helix: 0.53 (0.23), residues: 528 sheet: -1.41 (0.46), residues: 124 loop : -2.34 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 532 TYR 0.020 0.002 TYR A 499 PHE 0.047 0.002 PHE A 335 TRP 0.014 0.002 TRP C 466 HIS 0.009 0.001 HIS C 437 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 9862) covalent geometry : angle 0.67055 (13352) hydrogen bonds : bond 0.04273 ( 380) hydrogen bonds : angle 4.76866 ( 1131) metal coordination : bond 0.01052 ( 3) Misc. bond : bond 0.00185 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 222 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 ASP cc_start: 0.7157 (t0) cc_final: 0.6821 (t0) REVERT: B 50 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.6461 (mt0) REVERT: B 99 LEU cc_start: 0.7306 (mt) cc_final: 0.7064 (mp) REVERT: B 109 GLU cc_start: 0.6718 (mp0) cc_final: 0.6482 (mp0) REVERT: B 133 ASP cc_start: 0.6764 (t0) cc_final: 0.6163 (t0) REVERT: B 135 THR cc_start: 0.8403 (m) cc_final: 0.8104 (m) REVERT: B 229 ASN cc_start: 0.7966 (t0) cc_final: 0.7408 (t0) REVERT: A 86 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.6923 (p0) REVERT: A 136 ASN cc_start: 0.6862 (p0) cc_final: 0.6301 (m110) REVERT: A 181 LYS cc_start: 0.8172 (mmmt) cc_final: 0.7822 (mmtm) REVERT: A 191 SER cc_start: 0.8512 (m) cc_final: 0.8052 (p) REVERT: A 230 ASN cc_start: 0.7896 (m110) cc_final: 0.7575 (m110) REVERT: A 243 PHE cc_start: 0.7205 (t80) cc_final: 0.6788 (t80) REVERT: A 374 ASP cc_start: 0.7111 (t0) cc_final: 0.6875 (t0) REVERT: A 393 THR cc_start: 0.8065 (t) cc_final: 0.7840 (m) REVERT: A 418 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7390 (mt-10) REVERT: A 480 GLU cc_start: 0.6587 (mm-30) cc_final: 0.6372 (mm-30) REVERT: A 530 GLU cc_start: 0.7669 (tt0) cc_final: 0.7454 (pt0) REVERT: A 533 ILE cc_start: 0.7644 (tp) cc_final: 0.7434 (tt) REVERT: C 1 MET cc_start: 0.7127 (mtm) cc_final: 0.6625 (ppp) REVERT: C 74 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.6775 (m-10) REVERT: C 109 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7236 (mt) REVERT: C 127 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7478 (mp0) REVERT: C 155 ILE cc_start: 0.8286 (mp) cc_final: 0.8050 (mm) REVERT: C 163 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6771 (mp0) REVERT: C 398 ILE cc_start: 0.8225 (mt) cc_final: 0.7545 (mt) REVERT: C 416 ARG cc_start: 0.6628 (mtm110) cc_final: 0.5984 (mmp-170) REVERT: C 468 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7712 (tp) REVERT: C 470 ASN cc_start: 0.7520 (m110) cc_final: 0.6992 (m110) REVERT: C 537 ASP cc_start: 0.7666 (t0) cc_final: 0.7257 (t0) outliers start: 43 outliers final: 30 residues processed: 244 average time/residue: 0.1036 time to fit residues: 34.4248 Evaluate side-chains 254 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 218 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 245 ARG Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 506 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 28 optimal weight: 0.0970 chunk 24 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 57 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 64 optimal weight: 0.0020 chunk 108 optimal weight: 0.5980 chunk 102 optimal weight: 0.0370 overall best weight: 0.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS B 227 GLN C 60 GLN C 204 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.153739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.131244 restraints weight = 13642.966| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.41 r_work: 0.3655 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9867 Z= 0.118 Angle : 0.629 9.411 13352 Z= 0.319 Chirality : 0.042 0.154 1488 Planarity : 0.004 0.068 1718 Dihedral : 7.519 85.434 1369 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.74 % Favored : 89.01 % Rotamer: Outliers : 2.70 % Allowed : 18.92 % Favored : 78.38 % 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 aren not related in a simple way. whole: -1.22 (0.24), residues: 1210 helix: 0.78 (0.23), residues: 524 sheet: -1.54 (0.44), residues: 128 loop : -2.25 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 62 TYR 0.019 0.001 TYR A 499 PHE 0.033 0.001 PHE A 335 TRP 0.018 0.001 TRP C 466 HIS 0.009 0.001 HIS C 437 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9862) covalent geometry : angle 0.62851 (13352) hydrogen bonds : bond 0.03503 ( 380) hydrogen bonds : angle 4.51620 ( 1131) metal coordination : bond 0.00305 ( 3) Misc. bond : bond 0.00100 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 ASP cc_start: 0.7197 (t0) cc_final: 0.6869 (t0) REVERT: B 50 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6274 (mt0) REVERT: B 99 LEU cc_start: 0.7248 (mt) cc_final: 0.7018 (mp) REVERT: B 133 ASP cc_start: 0.6915 (t0) cc_final: 0.6276 (t0) REVERT: B 135 THR cc_start: 0.8379 (m) cc_final: 0.8084 (m) REVERT: B 229 ASN cc_start: 0.7854 (t0) cc_final: 0.7323 (t0) REVERT: A 83 MET cc_start: 0.7452 (mmt) cc_final: 0.7173 (mmt) REVERT: A 181 LYS cc_start: 0.8172 (mmmt) cc_final: 0.7861 (mmtm) REVERT: A 191 SER cc_start: 0.8472 (m) cc_final: 0.7992 (p) REVERT: A 230 ASN cc_start: 0.7898 (m110) cc_final: 0.7575 (m110) REVERT: A 243 PHE cc_start: 0.7005 (t80) cc_final: 0.6513 (t80) REVERT: A 374 ASP cc_start: 0.7017 (t0) cc_final: 0.6785 (t0) REVERT: A 469 GLU cc_start: 0.6988 (tm-30) cc_final: 0.6748 (tm-30) REVERT: A 480 GLU cc_start: 0.6575 (mm-30) cc_final: 0.6319 (mm-30) REVERT: A 533 ILE cc_start: 0.7614 (tp) cc_final: 0.7362 (tt) REVERT: C 1 MET cc_start: 0.7157 (mtm) cc_final: 0.6727 (ppp) REVERT: C 71 TYR cc_start: 0.7613 (t80) cc_final: 0.7370 (t80) REVERT: C 109 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7158 (mt) REVERT: C 127 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7582 (mp0) REVERT: C 398 ILE cc_start: 0.8193 (mt) cc_final: 0.7740 (mt) REVERT: C 416 ARG cc_start: 0.6574 (mtm110) cc_final: 0.5909 (mmp-170) REVERT: C 468 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7704 (tp) REVERT: C 470 ASN cc_start: 0.7504 (m110) cc_final: 0.7000 (m110) REVERT: C 537 ASP cc_start: 0.7655 (t0) cc_final: 0.7329 (t0) outliers start: 28 outliers final: 17 residues processed: 234 average time/residue: 0.1038 time to fit residues: 33.0281 Evaluate side-chains 231 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain C residue 506 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 64 optimal weight: 0.4980 chunk 109 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 73 optimal weight: 0.9980 chunk 54 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS A 86 ASN A 121 HIS A 514 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.151723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.129944 restraints weight = 13686.678| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.40 r_work: 0.3606 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 9867 Z= 0.209 Angle : 0.687 10.037 13352 Z= 0.353 Chirality : 0.045 0.144 1488 Planarity : 0.005 0.072 1718 Dihedral : 7.814 89.901 1369 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.07 % Favored : 88.76 % Rotamer: Outliers : 3.09 % Allowed : 19.21 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.24), residues: 1210 helix: 0.71 (0.23), residues: 523 sheet: -1.39 (0.46), residues: 126 loop : -2.27 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 150 TYR 0.018 0.002 TYR C 137 PHE 0.029 0.002 PHE A 335 TRP 0.018 0.002 TRP B 91 HIS 0.008 0.001 HIS C 437 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 9862) covalent geometry : angle 0.68739 (13352) hydrogen bonds : bond 0.04301 ( 380) hydrogen bonds : angle 4.66441 ( 1131) metal coordination : bond 0.01346 ( 3) Misc. bond : bond 0.00170 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 ASP cc_start: 0.7211 (t0) cc_final: 0.6866 (t0) REVERT: B 50 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.6468 (mt0) REVERT: B 109 GLU cc_start: 0.6763 (mp0) cc_final: 0.6526 (mp0) REVERT: B 133 ASP cc_start: 0.6900 (t0) cc_final: 0.6288 (t0) REVERT: B 229 ASN cc_start: 0.7987 (t0) cc_final: 0.7410 (t0) REVERT: B 241 ASP cc_start: 0.7613 (m-30) cc_final: 0.7365 (t0) REVERT: A 71 TYR cc_start: 0.7628 (t80) cc_final: 0.6979 (t80) REVERT: A 72 LYS cc_start: 0.7798 (tppt) cc_final: 0.7505 (tptt) REVERT: A 86 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.6870 (p0) REVERT: A 181 LYS cc_start: 0.8265 (mmmt) cc_final: 0.7920 (mmtm) REVERT: A 191 SER cc_start: 0.8492 (m) cc_final: 0.8026 (p) REVERT: A 230 ASN cc_start: 0.7926 (m110) cc_final: 0.7593 (m110) REVERT: A 243 PHE cc_start: 0.7138 (t80) cc_final: 0.6703 (t80) REVERT: A 328 MET cc_start: 0.7728 (mtm) cc_final: 0.7492 (ptp) REVERT: A 418 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7475 (mt-10) REVERT: A 469 GLU cc_start: 0.7005 (tm-30) cc_final: 0.6761 (tm-30) REVERT: A 532 ARG cc_start: 0.7274 (ttm-80) cc_final: 0.6978 (ttp-110) REVERT: A 533 ILE cc_start: 0.7567 (tp) cc_final: 0.7344 (tt) REVERT: C 1 MET cc_start: 0.7133 (mtm) cc_final: 0.6624 (ppp) REVERT: C 71 TYR cc_start: 0.7558 (t80) cc_final: 0.7274 (t80) REVERT: C 109 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7292 (mt) REVERT: C 127 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7535 (mp0) REVERT: C 398 ILE cc_start: 0.8240 (mt) cc_final: 0.7804 (mt) REVERT: C 416 ARG cc_start: 0.6637 (mtm110) cc_final: 0.6000 (mmp-170) REVERT: C 468 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7719 (tp) REVERT: C 470 ASN cc_start: 0.7477 (m110) cc_final: 0.6960 (m110) REVERT: C 537 ASP cc_start: 0.7675 (t0) cc_final: 0.7337 (t0) outliers start: 32 outliers final: 25 residues processed: 230 average time/residue: 0.1076 time to fit residues: 33.2200 Evaluate side-chains 236 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 448 LYS Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 506 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 95 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 61 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 10 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.150072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.127537 restraints weight = 13615.093| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.37 r_work: 0.3607 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 9867 Z= 0.259 Angle : 1.020 59.114 13352 Z= 0.583 Chirality : 0.047 0.496 1488 Planarity : 0.007 0.196 1718 Dihedral : 7.850 89.864 1369 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.40 % Favored : 88.35 % Rotamer: Outliers : 3.19 % Allowed : 19.31 % Favored : 77.51 % Cbeta Deviations : 0.09 % 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 aren not related in a simple way. whole: -1.26 (0.24), residues: 1210 helix: 0.71 (0.23), residues: 523 sheet: -1.41 (0.46), residues: 126 loop : -2.28 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 240 TYR 0.046 0.002 TYR C 28 PHE 0.026 0.002 PHE A 335 TRP 0.017 0.002 TRP B 91 HIS 0.319 0.007 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00549 ( 9862) covalent geometry : angle 1.02008 (13352) hydrogen bonds : bond 0.04300 ( 380) hydrogen bonds : angle 4.67082 ( 1131) metal coordination : bond 0.01222 ( 3) Misc. bond : bond 0.00176 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 209 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 ASP cc_start: 0.7447 (t0) cc_final: 0.7111 (t0) REVERT: B 50 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.6617 (mt0) REVERT: B 133 ASP cc_start: 0.7005 (t0) cc_final: 0.6417 (t0) REVERT: B 229 ASN cc_start: 0.8072 (t0) cc_final: 0.7497 (t0) REVERT: B 241 ASP cc_start: 0.7841 (m-30) cc_final: 0.7613 (t0) REVERT: A 71 TYR cc_start: 0.7772 (t80) cc_final: 0.7121 (t80) REVERT: A 72 LYS cc_start: 0.7896 (tppt) cc_final: 0.7663 (tptt) REVERT: A 86 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.6949 (p0) REVERT: A 136 ASN cc_start: 0.7122 (p0) cc_final: 0.6425 (m110) REVERT: A 164 ASP cc_start: 0.7671 (p0) cc_final: 0.7168 (p0) REVERT: A 181 LYS cc_start: 0.8338 (mmmt) cc_final: 0.7989 (mmtm) REVERT: A 191 SER cc_start: 0.8587 (m) cc_final: 0.8157 (p) REVERT: A 230 ASN cc_start: 0.8030 (m110) cc_final: 0.7676 (m110) REVERT: A 243 PHE cc_start: 0.7202 (t80) cc_final: 0.6775 (t80) REVERT: A 328 MET cc_start: 0.7790 (mtm) cc_final: 0.7582 (ptp) REVERT: A 374 ASP cc_start: 0.7300 (t0) cc_final: 0.6844 (t0) REVERT: A 418 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7720 (mt-10) REVERT: A 448 LYS cc_start: 0.8138 (tmtt) cc_final: 0.7896 (tmtt) REVERT: A 469 GLU cc_start: 0.7291 (tm-30) cc_final: 0.7036 (tm-30) REVERT: A 532 ARG cc_start: 0.7442 (ttm-80) cc_final: 0.7143 (ttp-110) REVERT: A 533 ILE cc_start: 0.7744 (tp) cc_final: 0.7503 (tt) REVERT: C 1 MET cc_start: 0.7172 (mtm) cc_final: 0.6666 (ppp) REVERT: C 71 TYR cc_start: 0.7707 (t80) cc_final: 0.7433 (t80) REVERT: C 109 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7368 (mt) REVERT: C 127 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7684 (mp0) REVERT: C 398 ILE cc_start: 0.8360 (mt) cc_final: 0.7921 (mt) REVERT: C 416 ARG cc_start: 0.6764 (mtm110) cc_final: 0.6034 (mmp-170) REVERT: C 468 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7848 (tp) REVERT: C 470 ASN cc_start: 0.7749 (m110) cc_final: 0.7232 (m110) outliers start: 33 outliers final: 25 residues processed: 224 average time/residue: 0.1053 time to fit residues: 32.0178 Evaluate side-chains 239 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 210 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 448 LYS Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 506 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 81 optimal weight: 0.0470 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 64 optimal weight: 0.0050 chunk 112 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 overall best weight: 0.4092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 ASN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.150092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.127702 restraints weight = 13636.875| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.31 r_work: 0.3612 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 9867 Z= 0.222 Angle : 0.985 59.187 13352 Z= 0.554 Chirality : 0.044 0.183 1488 Planarity : 0.006 0.142 1718 Dihedral : 7.823 89.892 1369 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.24 % Favored : 88.60 % Rotamer: Outliers : 3.28 % Allowed : 19.21 % Favored : 77.51 % Cbeta Deviations : 0.09 % 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 aren not related in a simple way. whole: -1.25 (0.24), residues: 1210 helix: 0.72 (0.23), residues: 523 sheet: -1.41 (0.46), residues: 126 loop : -2.28 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 202 TYR 0.023 0.002 TYR C 28 PHE 0.022 0.002 PHE A 335 TRP 0.016 0.001 TRP B 91 HIS 0.183 0.005 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 9862) covalent geometry : angle 0.98521 (13352) hydrogen bonds : bond 0.04240 ( 380) hydrogen bonds : angle 4.67049 ( 1131) metal coordination : bond 0.00837 ( 3) Misc. bond : bond 0.00136 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2448.53 seconds wall clock time: 42 minutes 42.71 seconds (2562.71 seconds total)