Starting phenix.real_space_refine on Sat Aug 23 00:45:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o4a_70091/08_2025/9o4a_70091.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o4a_70091/08_2025/9o4a_70091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o4a_70091/08_2025/9o4a_70091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o4a_70091/08_2025/9o4a_70091.map" model { file = "/net/cci-nas-00/data/ceres_data/9o4a_70091/08_2025/9o4a_70091.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o4a_70091/08_2025/9o4a_70091.cif" } resolution = 2.8 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= 0.001 sd= 0.021 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 26 5.16 5 C 5577 2.51 5 N 1513 2.21 5 O 1681 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8804 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3642 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 16, 'TRANS': 451} Chain breaks: 1 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 3, 'GLN:plan1': 2, 'GLU:plan': 4, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "B" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3685 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 17, 'TRANS': 451} Chain breaks: 2 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 6, 'GLN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1414 Classifications: {'peptide': 179} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7366 SG CYS C 54 41.568 72.744 80.506 1.00 74.59 S ATOM 7389 SG CYS C 57 40.585 69.847 78.320 1.00 65.10 S ATOM 7456 SG CYS C 98 41.420 73.428 76.922 1.00 40.90 S ATOM 7579 SG CYS C 116 38.120 72.374 78.190 1.00 66.73 S Time building chain proxies: 2.60, per 1000 atoms: 0.30 Number of scatterers: 8804 At special positions: 0 Unit cell: (81.75, 129.71, 112.27, 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 26 16.00 P 6 15.00 O 1681 8.00 N 1513 7.00 C 5577 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 349.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 601 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 57 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 98 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 116 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 54 " Number of angles added : 6 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 8 sheets defined 43.5% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 22 through 31 removed outlier: 4.139A pdb=" N GLN A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 27 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TYR A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 51 Processing helix chain 'A' and resid 97 through 113 removed outlier: 3.994A pdb=" N ILE A 101 " --> pdb=" O GLY A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 170 through 187 removed outlier: 3.664A pdb=" N SER A 178 " --> pdb=" O ASN A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 219 removed outlier: 4.088A pdb=" N GLU A 219 " --> pdb=" O GLU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.884A pdb=" N TYR A 229 " --> pdb=" O PHE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 252 Processing helix chain 'A' and resid 318 through 332 removed outlier: 3.551A pdb=" N VAL A 324 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 327 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N SER A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 Processing helix chain 'A' and resid 412 through 421 Processing helix chain 'A' and resid 440 through 442 No H-bonds generated for 'chain 'A' and resid 440 through 442' Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 484 through 495 Processing helix chain 'A' and resid 501 through 516 removed outlier: 3.599A pdb=" N HIS A 514 " --> pdb=" O THR A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 539 removed outlier: 3.593A pdb=" N GLU A 524 " --> pdb=" O GLU A 520 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 19 removed outlier: 3.613A pdb=" N LYS B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B 18 " --> pdb=" O LYS B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 31 removed outlier: 4.065A pdb=" N LEU B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS B 29 " --> pdb=" O TYR B 25 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL B 30 " --> pdb=" O GLN B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 55 Processing helix chain 'B' and resid 97 through 117 removed outlier: 3.607A pdb=" N GLY B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG B 115 " --> pdb=" O HIS B 111 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 172 through 187 Processing helix chain 'B' and resid 201 through 205 removed outlier: 4.020A pdb=" N ASN B 204 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASP B 205 " --> pdb=" O ARG B 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 201 through 205' Processing helix chain 'B' and resid 238 through 248 Processing helix chain 'B' and resid 318 through 332 removed outlier: 3.651A pdb=" N ALA B 327 " --> pdb=" O THR B 323 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 330 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 332 " --> pdb=" O MET B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 383 removed outlier: 3.699A pdb=" N ILE B 368 " --> pdb=" O GLY B 364 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 421 Processing helix chain 'B' and resid 432 through 437 Processing helix chain 'B' and resid 438 through 439 No H-bonds generated for 'chain 'B' and resid 438 through 439' Processing helix chain 'B' and resid 440 through 442 No H-bonds generated for 'chain 'B' and resid 440 through 442' Processing helix chain 'B' and resid 463 through 473 Processing helix chain 'B' and resid 481 through 496 removed outlier: 3.900A pdb=" N LEU B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 488 " --> pdb=" O THR B 484 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU B 489 " --> pdb=" O LYS B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 516 removed outlier: 3.517A pdb=" N GLY B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 538 removed outlier: 3.572A pdb=" N GLU B 524 " --> pdb=" O GLU B 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 128 removed outlier: 3.728A pdb=" N TYR C 119 " --> pdb=" O SER C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 192 Processing helix chain 'C' and resid 195 through 213 removed outlier: 4.067A pdb=" N LYS C 204 " --> pdb=" O ASN C 200 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU C 205 " --> pdb=" O ALA C 201 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU C 206 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE C 207 " --> pdb=" O ARG C 203 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS C 212 " --> pdb=" O HIS C 208 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA C 213 " --> pdb=" O PHE C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 229 Processing helix chain 'C' and resid 238 through 246 removed outlier: 4.079A pdb=" N ILE C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 256 removed outlier: 3.602A pdb=" N GLN C 251 " --> pdb=" O ASP C 247 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80 removed outlier: 3.649A pdb=" N LEU A 77 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASN A 143 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE A 66 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA A 141 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU A 68 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N SER A 139 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 197 through 198 removed outlier: 3.559A pdb=" N ILE A 427 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 398 " --> pdb=" O ILE A 427 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N THR A 88 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N TRP A 445 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE A 89 " --> pdb=" O TRP A 445 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU A 447 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 91 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 341 removed outlier: 5.642A pdb=" N ASN A 337 " --> pdb=" O ASP A 350 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP A 350 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP A 346 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 68 removed outlier: 4.969A pdb=" N VAL B 63 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ASP B 145 " --> pdb=" O VAL B 63 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 68 removed outlier: 4.969A pdb=" N VAL B 63 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ASP B 145 " --> pdb=" O VAL B 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 426 through 429 Processing sheet with id=AA7, first strand: chain 'B' and resid 197 through 198 removed outlier: 3.747A pdb=" N TYR B 198 " --> pdb=" O LEU B 397 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 335 through 341 removed outlier: 5.971A pdb=" N ASN B 337 " --> pdb=" O ASP B 350 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASP B 350 " --> pdb=" O ASN B 337 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN B 341 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP B 346 " --> pdb=" O GLN B 341 " (cutoff:3.500A) 342 hydrogen bonds defined for protein. 1002 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: 1.33 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2891 1.34 - 1.46: 1650 1.46 - 1.58: 4378 1.58 - 1.69: 16 1.69 - 1.81: 42 Bond restraints: 8977 Sorted by residual: bond pdb=" C4' ATP B 601 " pdb=" O4' ATP B 601 " ideal model delta sigma weight residual 1.444 1.703 -0.259 1.10e-02 8.26e+03 5.54e+02 bond pdb=" C4' ATP A 601 " pdb=" O4' ATP A 601 " ideal model delta sigma weight residual 1.444 1.702 -0.258 1.10e-02 8.26e+03 5.51e+02 bond pdb=" C3' ATP B 601 " pdb=" C4' ATP B 601 " ideal model delta sigma weight residual 1.526 1.303 0.223 1.10e-02 8.26e+03 4.10e+02 bond pdb=" C3' ATP A 601 " pdb=" C4' ATP A 601 " ideal model delta sigma weight residual 1.526 1.304 0.222 1.10e-02 8.26e+03 4.07e+02 bond pdb=" C6 ATP A 601 " pdb=" N6 ATP A 601 " ideal model delta sigma weight residual 1.337 1.487 -0.150 1.10e-02 8.26e+03 1.86e+02 ... (remaining 8972 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 12013 3.26 - 6.51: 117 6.51 - 9.77: 23 9.77 - 13.02: 3 13.02 - 16.28: 3 Bond angle restraints: 12159 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 123.59 16.28 1.00e+00 1.00e+00 2.65e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 124.81 15.06 1.00e+00 1.00e+00 2.27e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 125.10 11.73 1.00e+00 1.00e+00 1.38e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 125.97 10.86 1.00e+00 1.00e+00 1.18e+02 angle pdb=" C5 ATP A 601 " pdb=" C4 ATP A 601 " pdb=" N3 ATP A 601 " ideal model delta sigma weight residual 126.80 119.20 7.60 1.00e+00 1.00e+00 5.77e+01 ... (remaining 12154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4984 17.99 - 35.98: 377 35.98 - 53.97: 52 53.97 - 71.96: 31 71.96 - 89.95: 5 Dihedral angle restraints: 5449 sinusoidal: 2198 harmonic: 3251 Sorted by residual: dihedral pdb=" CA PHE A 472 " pdb=" C PHE A 472 " pdb=" N GLU A 473 " pdb=" CA GLU A 473 " ideal model delta harmonic sigma weight residual -180.00 -151.48 -28.52 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA PRO B 344 " pdb=" C PRO B 344 " pdb=" N LEU B 345 " pdb=" CA LEU B 345 " ideal model delta harmonic sigma weight residual -180.00 -152.90 -27.10 0 5.00e+00 4.00e-02 2.94e+01 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 -153.12 -26.88 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 5446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1087 0.054 - 0.108: 232 0.108 - 0.162: 43 0.162 - 0.217: 2 0.217 - 0.271: 3 Chirality restraints: 1367 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 -2.36 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C3' ATP B 601 " pdb=" C2' ATP B 601 " pdb=" C4' ATP B 601 " pdb=" O3' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE B 78 " pdb=" CA ILE B 78 " pdb=" CG1 ILE B 78 " pdb=" CG2 ILE B 78 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1364 not shown) Planarity restraints: 1555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 534 " 0.025 2.00e-02 2.50e+03 1.91e-02 9.15e+00 pdb=" CG TRP A 534 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 534 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 534 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 534 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 534 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 534 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 534 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 534 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 534 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 383 " 0.050 5.00e-02 4.00e+02 7.49e-02 8.97e+00 pdb=" N PRO B 384 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 384 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 384 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 478 " 0.042 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO B 479 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 479 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 479 " 0.035 5.00e-02 4.00e+02 ... (remaining 1552 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1739 2.78 - 3.31: 8430 3.31 - 3.84: 14245 3.84 - 4.37: 17007 4.37 - 4.90: 28979 Nonbonded interactions: 70400 Sorted by model distance: nonbonded pdb=" OG SER B 441 " pdb=" O PRO B 456 " model vdw 2.246 3.040 nonbonded pdb=" OE1 GLU B 201 " pdb=" ND2 ASN B 204 " model vdw 2.251 3.120 nonbonded pdb=" O PHE A 48 " pdb=" OG SER A 52 " model vdw 2.297 3.040 nonbonded pdb=" O PRO B 193 " pdb=" OH TYR B 229 " model vdw 2.337 3.040 nonbonded pdb=" O LYS B 107 " pdb=" OG1 THR B 110 " model vdw 2.345 3.040 ... (remaining 70395 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 11 through 15 and (name N or name CA or name C or name O \ or name CB )) or resid 16 or (resid 17 and (name N or name CA or name C or name \ O or name CB )) or resid 18 through 26 or (resid 27 and (name N or name CA or na \ me C or name O or name CB )) or resid 28 or (resid 29 and (name N or name CA or \ name C or name O or name CB )) or resid 30 through 32 or resid 39 through 56 or \ (resid 57 and (name N or name CA or name C or name O or name CB )) or resid 58 t \ hrough 123 or (resid 124 and (name N or name CA or name C or name O or name CB ) \ ) or resid 125 through 534 or (resid 535 and (name N or name CA or name C or nam \ e O or name CB )) or resid 536 through 538 or (resid 539 and (name N or name CA \ or name C or name O or name CB )) or resid 601)) selection = (chain 'B' and ((resid 11 through 15 and (name N or name CA or name C or name O \ or name CB )) or resid 16 through 20 or (resid 21 through 22 and (name N or name \ CA or name C or name O or name CB )) or resid 23 through 24 or (resid 25 throug \ h 27 and (name N or name CA or name C or name O or name CB )) or resid 28 throug \ h 43 or (resid 44 and (name N or name CA or name C or name O or name CB )) or re \ sid 45 through 46 or (resid 47 and (name N or name CA or name C or name O or nam \ e CB )) or resid 48 through 53 or (resid 54 through 55 and (name N or name CA or \ name C or name O or name CB )) or resid 56 through 166 or (resid 167 and (name \ N or name CA or name C or name O or name CB )) or resid 168 through 209 or (resi \ d 210 and (name N or name CA or name C or name O or name CB )) or resid 211 thro \ ugh 254 or resid 317 through 318 or (resid 319 and (name N or name CA or name C \ or name O or name CB )) or resid 320 through 403 or (resid 404 and (name N or na \ me CA or name C or name O or name CB )) or resid 405 through 479 or (resid 480 a \ nd (name N or name CA or name C or name O or name CB )) or resid 481 through 601 \ )) } 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.180 Find NCS groups from input model: 0.150 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: 0.000 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 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 : 0.008 0.259 8981 Z= 0.621 Angle : 0.860 17.229 12165 Z= 0.535 Chirality : 0.046 0.271 1367 Planarity : 0.005 0.075 1555 Dihedral : 13.616 89.951 3341 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.26 % Favored : 90.65 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.88 (0.25), residues: 1102 helix: -0.22 (0.24), residues: 465 sheet: -0.88 (0.53), residues: 113 loop : -2.32 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 532 TYR 0.011 0.001 TYR B 229 PHE 0.020 0.001 PHE A 538 TRP 0.050 0.002 TRP A 534 HIS 0.010 0.002 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00755 ( 8977) covalent geometry : angle 0.83519 (12159) hydrogen bonds : bond 0.16016 ( 338) hydrogen bonds : angle 7.31244 ( 1002) metal coordination : bond 0.00839 ( 4) metal coordination : angle 9.22838 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 162 TYR cc_start: 0.7507 (m-80) cc_final: 0.7084 (m-80) REVERT: A 163 GLU cc_start: 0.8206 (mp0) cc_final: 0.7768 (mp0) REVERT: A 251 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6596 (mm-30) REVERT: A 341 GLN cc_start: 0.7711 (tt0) cc_final: 0.7342 (tt0) REVERT: A 497 GLU cc_start: 0.7762 (pt0) cc_final: 0.7491 (pm20) REVERT: B 91 VAL cc_start: 0.8521 (t) cc_final: 0.8288 (m) REVERT: B 93 ASN cc_start: 0.8176 (m-40) cc_final: 0.7857 (m-40) REVERT: B 251 GLU cc_start: 0.7382 (mt-10) cc_final: 0.6766 (tt0) REVERT: B 365 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6958 (pt0) REVERT: B 379 LEU cc_start: 0.7799 (mt) cc_final: 0.7565 (tp) REVERT: B 487 LEU cc_start: 0.7882 (tp) cc_final: 0.7621 (tm) REVERT: C 60 ASP cc_start: 0.7610 (t0) cc_final: 0.7375 (t0) REVERT: C 123 TYR cc_start: 0.7536 (t80) cc_final: 0.7282 (t80) outliers start: 0 outliers final: 1 residues processed: 248 average time/residue: 0.5613 time to fit residues: 148.5769 Evaluate side-chains 200 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 199 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.0870 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.0060 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.0770 chunk 106 optimal weight: 0.5980 overall best weight: 0.2932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 135 GLN A 204 ASN A 410 GLN ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 HIS A 449 ASN A 451 GLN B 187 ASN B 204 ASN B 230 ASN C 194 ASN ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 ASN C 229 ASN C 255 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.158865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.142544 restraints weight = 11827.426| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.79 r_work: 0.3831 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8981 Z= 0.126 Angle : 0.665 12.830 12165 Z= 0.337 Chirality : 0.044 0.155 1367 Planarity : 0.005 0.077 1555 Dihedral : 9.413 84.214 1259 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 2.88 % Allowed : 9.49 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.59 (0.25), residues: 1102 helix: 0.07 (0.24), residues: 478 sheet: -0.96 (0.47), residues: 131 loop : -2.24 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 342 TYR 0.011 0.001 TYR B 229 PHE 0.034 0.002 PHE B 538 TRP 0.027 0.001 TRP A 534 HIS 0.005 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8977) covalent geometry : angle 0.64474 (12159) hydrogen bonds : bond 0.04224 ( 338) hydrogen bonds : angle 5.13554 ( 1002) metal coordination : bond 0.00680 ( 4) metal coordination : angle 7.35934 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TYR cc_start: 0.7591 (m-80) cc_final: 0.7206 (m-80) REVERT: A 209 ARG cc_start: 0.7784 (mtm110) cc_final: 0.7508 (mtt90) REVERT: A 251 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6710 (mm-30) REVERT: A 342 ARG cc_start: 0.7314 (mmm160) cc_final: 0.6950 (mmm160) REVERT: A 365 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6650 (mt-10) REVERT: A 497 GLU cc_start: 0.7848 (pt0) cc_final: 0.7568 (pm20) REVERT: A 535 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: B 105 ILE cc_start: 0.7729 (mt) cc_final: 0.7497 (tt) REVERT: B 234 THR cc_start: 0.7959 (p) cc_final: 0.7749 (t) REVERT: B 326 ASP cc_start: 0.8079 (m-30) cc_final: 0.7797 (m-30) REVERT: B 524 GLU cc_start: 0.6353 (mt-10) cc_final: 0.6073 (mt-10) REVERT: C 60 ASP cc_start: 0.7663 (t0) cc_final: 0.7393 (t0) outliers start: 27 outliers final: 6 residues processed: 211 average time/residue: 0.5872 time to fit residues: 132.0132 Evaluate side-chains 191 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 184 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain C residue 226 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 72 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 411 GLN A 425 GLN A 437 HIS A 449 ASN B 67 HIS ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 ASN B 204 ASN B 221 GLN C 168 ASN C 229 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.154458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.137935 restraints weight = 11755.749| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 1.81 r_work: 0.3783 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8981 Z= 0.172 Angle : 0.657 8.950 12165 Z= 0.337 Chirality : 0.044 0.149 1367 Planarity : 0.005 0.073 1555 Dihedral : 9.310 76.447 1257 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 3.20 % Allowed : 14.18 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.42 (0.25), residues: 1102 helix: 0.22 (0.24), residues: 472 sheet: -1.00 (0.46), residues: 133 loop : -2.09 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 342 TYR 0.016 0.001 TYR B 229 PHE 0.023 0.002 PHE B 538 TRP 0.020 0.002 TRP A 534 HIS 0.006 0.001 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 8977) covalent geometry : angle 0.64430 (12159) hydrogen bonds : bond 0.04263 ( 338) hydrogen bonds : angle 4.75970 ( 1002) metal coordination : bond 0.00773 ( 4) metal coordination : angle 5.91134 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.8102 (p0) cc_final: 0.7860 (p0) REVERT: A 143 ASN cc_start: 0.7886 (m-40) cc_final: 0.7599 (m110) REVERT: A 209 ARG cc_start: 0.7865 (mtm110) cc_final: 0.7560 (mtt90) REVERT: A 226 PHE cc_start: 0.7166 (m-10) cc_final: 0.6951 (m-10) REVERT: A 236 LYS cc_start: 0.8313 (mtmt) cc_final: 0.8076 (mppt) REVERT: A 365 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6770 (mt-10) REVERT: A 497 GLU cc_start: 0.7801 (pt0) cc_final: 0.7577 (pm20) REVERT: A 535 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: B 65 ASP cc_start: 0.7603 (p0) cc_final: 0.7331 (p0) REVERT: B 105 ILE cc_start: 0.7809 (mt) cc_final: 0.7557 (tt) REVERT: B 524 GLU cc_start: 0.6641 (mt-10) cc_final: 0.6321 (mt-10) REVERT: C 123 TYR cc_start: 0.7626 (t80) cc_final: 0.7335 (t80) outliers start: 30 outliers final: 9 residues processed: 196 average time/residue: 0.6283 time to fit residues: 130.9680 Evaluate side-chains 189 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 179 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 480 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 105 optimal weight: 0.0670 chunk 54 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 ASN B 135 GLN B 187 ASN ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 HIS C 229 ASN C 255 ASN 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 = 0.152971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.136288 restraints weight = 11835.749| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.80 r_work: 0.3765 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8981 Z= 0.172 Angle : 0.634 8.665 12165 Z= 0.330 Chirality : 0.044 0.144 1367 Planarity : 0.005 0.070 1555 Dihedral : 8.393 77.954 1257 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 3.41 % Allowed : 15.88 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.37 (0.25), residues: 1102 helix: 0.31 (0.24), residues: 472 sheet: -1.04 (0.48), residues: 127 loop : -2.10 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 342 TYR 0.012 0.001 TYR B 229 PHE 0.017 0.002 PHE B 538 TRP 0.013 0.002 TRP A 534 HIS 0.005 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 8977) covalent geometry : angle 0.62593 (12159) hydrogen bonds : bond 0.04198 ( 338) hydrogen bonds : angle 4.56279 ( 1002) metal coordination : bond 0.00823 ( 4) metal coordination : angle 4.46788 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7429 (mp0) cc_final: 0.7140 (mp0) REVERT: A 153 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6730 (ttt) REVERT: A 209 ARG cc_start: 0.7871 (mtm110) cc_final: 0.7582 (mtt90) REVERT: A 236 LYS cc_start: 0.8321 (mtmt) cc_final: 0.7872 (mttp) REVERT: A 513 GLN cc_start: 0.7767 (mt0) cc_final: 0.7561 (mt0) REVERT: A 524 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6421 (mm-30) REVERT: A 535 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: B 62 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7296 (mmt-90) REVERT: B 105 ILE cc_start: 0.7844 (mt) cc_final: 0.7582 (tt) REVERT: B 524 GLU cc_start: 0.6772 (mt-10) cc_final: 0.6519 (mt-10) REVERT: C 123 TYR cc_start: 0.7627 (t80) cc_final: 0.7421 (t80) outliers start: 32 outliers final: 16 residues processed: 204 average time/residue: 0.5978 time to fit residues: 129.8007 Evaluate side-chains 201 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 476 GLN Chi-restraints excluded: chain B residue 480 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 25 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 ASN B 187 ASN ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN C 255 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.151305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.134716 restraints weight = 11791.051| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.79 r_work: 0.3745 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8981 Z= 0.201 Angle : 0.656 9.781 12165 Z= 0.344 Chirality : 0.045 0.145 1367 Planarity : 0.005 0.070 1555 Dihedral : 8.144 80.701 1257 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 3.84 % Allowed : 17.27 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.40 (0.25), residues: 1102 helix: 0.26 (0.24), residues: 475 sheet: -1.05 (0.47), residues: 127 loop : -2.10 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 342 TYR 0.016 0.001 TYR B 229 PHE 0.030 0.002 PHE B 538 TRP 0.013 0.002 TRP B 245 HIS 0.006 0.001 HIS C 148 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 8977) covalent geometry : angle 0.64827 (12159) hydrogen bonds : bond 0.04472 ( 338) hydrogen bonds : angle 4.60856 ( 1002) metal coordination : bond 0.00934 ( 4) metal coordination : angle 4.68055 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7405 (mp0) cc_final: 0.7051 (mp0) REVERT: A 153 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6834 (ttt) REVERT: A 209 ARG cc_start: 0.7814 (mtm110) cc_final: 0.7565 (mtt90) REVERT: A 221 GLN cc_start: 0.6588 (OUTLIER) cc_final: 0.5633 (mp10) REVERT: A 236 LYS cc_start: 0.8337 (mtmt) cc_final: 0.7985 (mttt) REVERT: A 524 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6583 (mm-30) REVERT: A 532 ARG cc_start: 0.7720 (mtp85) cc_final: 0.7423 (mtp85) REVERT: A 535 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: B 65 ASP cc_start: 0.7664 (p0) cc_final: 0.7412 (p0) REVERT: B 105 ILE cc_start: 0.7875 (mt) cc_final: 0.7599 (tt) REVERT: B 130 GLU cc_start: 0.6935 (mt-10) cc_final: 0.6699 (mt-10) REVERT: B 524 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6613 (mt-10) outliers start: 36 outliers final: 18 residues processed: 189 average time/residue: 0.6266 time to fit residues: 125.7438 Evaluate side-chains 194 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 476 GLN Chi-restraints excluded: chain C residue 54 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 86 optimal weight: 0.0870 chunk 39 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 ASN ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN C 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.152395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.135906 restraints weight = 11885.381| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.81 r_work: 0.3750 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8981 Z= 0.176 Angle : 0.645 9.302 12165 Z= 0.336 Chirality : 0.044 0.153 1367 Planarity : 0.005 0.067 1555 Dihedral : 8.112 82.428 1257 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 2.77 % Allowed : 20.04 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.29 (0.25), residues: 1102 helix: 0.42 (0.24), residues: 476 sheet: -1.14 (0.48), residues: 117 loop : -2.06 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 342 TYR 0.012 0.001 TYR B 229 PHE 0.023 0.002 PHE B 538 TRP 0.012 0.001 TRP B 245 HIS 0.005 0.001 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 8977) covalent geometry : angle 0.63759 (12159) hydrogen bonds : bond 0.04129 ( 338) hydrogen bonds : angle 4.48131 ( 1002) metal coordination : bond 0.00781 ( 4) metal coordination : angle 4.54913 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7391 (mp0) cc_final: 0.6824 (mp0) REVERT: A 153 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6831 (ttt) REVERT: A 201 GLU cc_start: 0.7520 (pt0) cc_final: 0.7260 (OUTLIER) REVERT: A 209 ARG cc_start: 0.7819 (mtm110) cc_final: 0.7572 (mtt90) REVERT: A 236 LYS cc_start: 0.8340 (mtmt) cc_final: 0.8012 (mppt) REVERT: A 365 GLU cc_start: 0.7286 (mt-10) cc_final: 0.7085 (mt-10) REVERT: A 448 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.8025 (ttpm) REVERT: A 524 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6552 (mm-30) REVERT: A 532 ARG cc_start: 0.7712 (mtp85) cc_final: 0.7390 (mtp85) REVERT: A 535 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: B 65 ASP cc_start: 0.7664 (p0) cc_final: 0.7418 (p0) REVERT: B 105 ILE cc_start: 0.7858 (mt) cc_final: 0.7579 (tt) REVERT: B 130 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6730 (mt-10) REVERT: B 359 LEU cc_start: 0.8396 (tt) cc_final: 0.8174 (tp) REVERT: B 524 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6596 (mt-10) REVERT: C 107 ASP cc_start: 0.7381 (t0) cc_final: 0.7008 (t0) outliers start: 26 outliers final: 17 residues processed: 189 average time/residue: 0.6258 time to fit residues: 125.6226 Evaluate side-chains 194 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 448 LYS Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 476 GLN Chi-restraints excluded: chain C residue 54 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 57 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 0.0170 chunk 100 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 94 optimal weight: 0.0040 chunk 46 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 overall best weight: 0.5230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 ASN ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN C 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.153020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.136566 restraints weight = 11930.199| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.81 r_work: 0.3755 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8981 Z= 0.153 Angle : 0.629 8.531 12165 Z= 0.328 Chirality : 0.043 0.157 1367 Planarity : 0.005 0.064 1555 Dihedral : 7.946 81.031 1257 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 3.20 % Allowed : 20.26 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.17 (0.25), residues: 1102 helix: 0.59 (0.24), residues: 476 sheet: -1.10 (0.48), residues: 115 loop : -2.07 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 342 TYR 0.011 0.001 TYR B 229 PHE 0.022 0.002 PHE B 538 TRP 0.011 0.001 TRP B 245 HIS 0.005 0.001 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8977) covalent geometry : angle 0.62207 (12159) hydrogen bonds : bond 0.03890 ( 338) hydrogen bonds : angle 4.37610 ( 1002) metal coordination : bond 0.00668 ( 4) metal coordination : angle 4.19771 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7377 (mp0) cc_final: 0.6819 (mp0) REVERT: A 153 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6772 (ttt) REVERT: A 201 GLU cc_start: 0.7507 (pt0) cc_final: 0.7218 (pt0) REVERT: A 236 LYS cc_start: 0.8321 (mtmt) cc_final: 0.7953 (mppt) REVERT: A 448 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8041 (ttpm) REVERT: A 524 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6552 (mm-30) REVERT: A 535 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: B 65 ASP cc_start: 0.7662 (p0) cc_final: 0.7415 (p0) REVERT: B 105 ILE cc_start: 0.7850 (mt) cc_final: 0.7561 (tt) REVERT: B 130 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6700 (mt-10) REVERT: B 219 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6824 (mt-10) REVERT: B 359 LEU cc_start: 0.8407 (tt) cc_final: 0.8186 (tp) REVERT: B 524 GLU cc_start: 0.6865 (mt-10) cc_final: 0.6556 (mt-10) outliers start: 30 outliers final: 18 residues processed: 189 average time/residue: 0.6070 time to fit residues: 122.0952 Evaluate side-chains 189 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 448 LYS Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 476 GLN Chi-restraints excluded: chain B residue 505 ARG Chi-restraints excluded: chain C residue 54 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 17 optimal weight: 0.4980 chunk 103 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 0.0030 chunk 65 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 ASN ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN C 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.151933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.135374 restraints weight = 11771.044| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.78 r_work: 0.3757 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8981 Z= 0.159 Angle : 0.638 8.426 12165 Z= 0.332 Chirality : 0.043 0.156 1367 Planarity : 0.005 0.060 1555 Dihedral : 7.859 81.769 1257 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 3.30 % Allowed : 21.22 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.13 (0.25), residues: 1102 helix: 0.62 (0.24), residues: 476 sheet: -1.02 (0.47), residues: 123 loop : -2.09 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 209 TYR 0.011 0.001 TYR B 229 PHE 0.024 0.002 PHE B 538 TRP 0.011 0.001 TRP B 245 HIS 0.005 0.001 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 8977) covalent geometry : angle 0.63103 (12159) hydrogen bonds : bond 0.03903 ( 338) hydrogen bonds : angle 4.36267 ( 1002) metal coordination : bond 0.00693 ( 4) metal coordination : angle 4.16537 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7550 (mptt) REVERT: A 127 GLU cc_start: 0.7373 (mp0) cc_final: 0.6812 (mp0) REVERT: A 153 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6811 (ttt) REVERT: A 201 GLU cc_start: 0.7504 (pt0) cc_final: 0.7158 (pt0) REVERT: A 236 LYS cc_start: 0.8339 (mtmt) cc_final: 0.7945 (mppt) REVERT: A 365 GLU cc_start: 0.7315 (mt-10) cc_final: 0.7079 (mt-10) REVERT: A 448 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.8037 (ttpm) REVERT: A 524 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6574 (mm-30) REVERT: A 535 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: B 65 ASP cc_start: 0.7648 (p0) cc_final: 0.7389 (p0) REVERT: B 105 ILE cc_start: 0.7845 (mt) cc_final: 0.7553 (tt) REVERT: B 130 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6688 (mt-10) REVERT: B 210 ASP cc_start: 0.7328 (m-30) cc_final: 0.7056 (p0) REVERT: B 219 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6843 (mt-10) REVERT: B 323 THR cc_start: 0.7765 (t) cc_final: 0.7541 (m) REVERT: B 356 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8360 (pt) REVERT: B 359 LEU cc_start: 0.8482 (tt) cc_final: 0.8259 (tp) REVERT: B 524 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6562 (mt-10) outliers start: 31 outliers final: 15 residues processed: 190 average time/residue: 0.6133 time to fit residues: 123.8489 Evaluate side-chains 189 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 448 LYS Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 476 GLN Chi-restraints excluded: chain C residue 54 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 37 optimal weight: 0.9980 chunk 88 optimal weight: 0.0370 chunk 36 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 chunk 33 optimal weight: 0.0770 chunk 87 optimal weight: 0.5980 chunk 27 optimal weight: 0.0980 chunk 1 optimal weight: 0.7980 chunk 95 optimal weight: 0.0000 overall best weight: 0.1620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 ASN ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN C 255 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.155922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.139584 restraints weight = 11763.447| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.82 r_work: 0.3779 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8981 Z= 0.112 Angle : 0.613 10.216 12165 Z= 0.317 Chirality : 0.042 0.149 1367 Planarity : 0.005 0.059 1555 Dihedral : 7.489 78.377 1257 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 2.77 % Allowed : 21.86 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.83 (0.26), residues: 1102 helix: 0.96 (0.25), residues: 468 sheet: -0.61 (0.51), residues: 107 loop : -2.01 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 342 TYR 0.006 0.001 TYR A 483 PHE 0.015 0.001 PHE A 246 TRP 0.010 0.001 TRP B 245 HIS 0.005 0.001 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8977) covalent geometry : angle 0.60910 (12159) hydrogen bonds : bond 0.03179 ( 338) hydrogen bonds : angle 4.19118 ( 1002) metal coordination : bond 0.00403 ( 4) metal coordination : angle 3.17587 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7388 (mp0) cc_final: 0.6820 (mp0) REVERT: A 153 MET cc_start: 0.7013 (OUTLIER) cc_final: 0.6685 (ttt) REVERT: A 201 GLU cc_start: 0.7497 (pt0) cc_final: 0.7159 (pt0) REVERT: A 236 LYS cc_start: 0.8344 (mtmt) cc_final: 0.7939 (mppt) REVERT: A 524 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6571 (mm-30) REVERT: A 535 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: B 65 ASP cc_start: 0.7620 (p0) cc_final: 0.7373 (p0) REVERT: B 105 ILE cc_start: 0.7784 (mt) cc_final: 0.7538 (tt) REVERT: B 219 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6812 (mt-10) REVERT: B 323 THR cc_start: 0.7737 (t) cc_final: 0.7499 (m) REVERT: B 524 GLU cc_start: 0.6647 (mt-10) cc_final: 0.6332 (mt-10) REVERT: C 107 ASP cc_start: 0.7211 (t0) cc_final: 0.6914 (t0) outliers start: 26 outliers final: 11 residues processed: 186 average time/residue: 0.6025 time to fit residues: 119.2720 Evaluate side-chains 188 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 476 GLN Chi-restraints excluded: chain B residue 505 ARG Chi-restraints excluded: chain C residue 54 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 85 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 0.0020 chunk 32 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 2 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 230 ASN A 411 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 ASN ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.151346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.134709 restraints weight = 11724.330| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.78 r_work: 0.3766 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8981 Z= 0.143 Angle : 0.640 8.108 12165 Z= 0.330 Chirality : 0.043 0.149 1367 Planarity : 0.005 0.071 1555 Dihedral : 7.571 83.508 1257 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 2.13 % Allowed : 23.13 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.86 (0.26), residues: 1102 helix: 0.88 (0.24), residues: 475 sheet: -0.87 (0.50), residues: 117 loop : -1.96 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 342 TYR 0.009 0.001 TYR B 229 PHE 0.023 0.002 PHE B 243 TRP 0.011 0.001 TRP B 245 HIS 0.006 0.001 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8977) covalent geometry : angle 0.63463 (12159) hydrogen bonds : bond 0.03651 ( 338) hydrogen bonds : angle 4.26600 ( 1002) metal coordination : bond 0.00614 ( 4) metal coordination : angle 3.68646 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7511 (mptt) REVERT: A 127 GLU cc_start: 0.7414 (mp0) cc_final: 0.6842 (mp0) REVERT: A 153 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6802 (ttt) REVERT: A 201 GLU cc_start: 0.7468 (pt0) cc_final: 0.7161 (pt0) REVERT: A 219 GLU cc_start: 0.6524 (tm-30) cc_final: 0.6312 (tm-30) REVERT: A 236 LYS cc_start: 0.8341 (mtmt) cc_final: 0.7969 (mppt) REVERT: A 448 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.8012 (ttpm) REVERT: A 524 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6598 (mm-30) REVERT: A 535 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: B 105 ILE cc_start: 0.7821 (mt) cc_final: 0.7555 (tt) REVERT: B 130 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6566 (mt-10) REVERT: B 219 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6871 (mt-10) REVERT: B 323 THR cc_start: 0.7739 (t) cc_final: 0.7513 (m) REVERT: B 524 GLU cc_start: 0.6859 (mt-10) cc_final: 0.6525 (mt-10) REVERT: C 107 ASP cc_start: 0.7256 (t0) cc_final: 0.6969 (t0) outliers start: 20 outliers final: 10 residues processed: 181 average time/residue: 0.6055 time to fit residues: 116.5797 Evaluate side-chains 181 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 448 LYS Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 505 ARG Chi-restraints excluded: chain C residue 54 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 76 optimal weight: 0.7980 chunk 98 optimal weight: 0.0020 chunk 84 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 33 optimal weight: 0.3980 chunk 26 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 0.0470 overall best weight: 0.3286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 ASN ** B 221 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 = 0.4071 r_free = 0.4071 target = 0.152532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.135955 restraints weight = 11721.452| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 1.80 r_work: 0.3781 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8981 Z= 0.124 Angle : 0.618 7.262 12165 Z= 0.319 Chirality : 0.043 0.150 1367 Planarity : 0.005 0.080 1555 Dihedral : 7.584 85.087 1257 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 2.24 % Allowed : 23.13 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.74 (0.26), residues: 1102 helix: 1.01 (0.25), residues: 469 sheet: -0.59 (0.48), residues: 121 loop : -1.96 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 342 TYR 0.007 0.001 TYR B 229 PHE 0.030 0.002 PHE A 246 TRP 0.011 0.001 TRP B 445 HIS 0.005 0.001 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8977) covalent geometry : angle 0.61325 (12159) hydrogen bonds : bond 0.03406 ( 338) hydrogen bonds : angle 4.20904 ( 1002) metal coordination : bond 0.00503 ( 4) metal coordination : angle 3.39717 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3844.15 seconds wall clock time: 66 minutes 23.39 seconds (3983.39 seconds total)