Starting phenix.real_space_refine on Wed Mar 4 11:50:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6l2t_0814/03_2026/6l2t_0814.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l2t_0814/03_2026/6l2t_0814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6l2t_0814/03_2026/6l2t_0814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l2t_0814/03_2026/6l2t_0814.map" model { file = "/net/cci-nas-00/data/ceres_data/6l2t_0814/03_2026/6l2t_0814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l2t_0814/03_2026/6l2t_0814.cif" } resolution = 4.1 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= 0.038 sd= 1.120 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: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 8728 2.51 5 N 2362 2.21 5 O 2467 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13604 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4511 Classifications: {'peptide': 628} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 48, 'TRANS': 579} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 556 Unresolved non-hydrogen angles: 702 Unresolved non-hydrogen dihedrals: 456 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'ASP:plan': 22, 'ASN:plan1': 9, 'GLU:plan': 16, 'GLN:plan1': 10, 'HIS:plan': 7, 'ARG:plan': 15, 'TYR:plan': 3, 'TRP:plan': 1, 'PHE:plan': 7} Unresolved non-hydrogen planarities: 379 Chain: "B" Number of atoms: 4554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4554 Classifications: {'peptide': 628} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 48, 'TRANS': 579} Chain breaks: 1 Unresolved non-hydrogen bonds: 511 Unresolved non-hydrogen angles: 643 Unresolved non-hydrogen dihedrals: 423 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ASP:plan': 19, 'GLU:plan': 16, 'GLN:plan1': 10, 'HIS:plan': 7, 'ARG:plan': 15, 'ASN:plan1': 8, 'TYR:plan': 3, 'TRP:plan': 1, 'PHE:plan': 7} Unresolved non-hydrogen planarities: 367 Chain: "C" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4539 Classifications: {'peptide': 633} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 48, 'TRANS': 584} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 553 Unresolved non-hydrogen angles: 695 Unresolved non-hydrogen dihedrals: 459 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'PHE:plan': 7, 'ASP:plan': 24, 'GLU:plan': 16, 'HIS:plan': 8, 'GLN:plan1': 9, 'ARG:plan': 16, 'ASN:plan1': 7, 'TYR:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 385 Time building chain proxies: 3.37, per 1000 atoms: 0.25 Number of scatterers: 13604 At special positions: 0 Unit cell: (95.85, 98.55, 132.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 2467 8.00 N 2362 7.00 C 8728 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: 0.93 Conformation dependent library (CDL) restraints added in 690.5 milliseconds 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 26 sheets defined 11.5% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 17 through 22 Processing helix chain 'A' and resid 22 through 40 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 183 through 187 removed outlier: 3.724A pdb=" N LEU A 187 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 removed outlier: 4.136A pdb=" N LYS A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 228 removed outlier: 3.976A pdb=" N TYR A 224 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 228 " --> pdb=" O TYR A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 422 through 426 removed outlier: 3.874A pdb=" N ASN A 425 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 476 No H-bonds generated for 'chain 'A' and resid 474 through 476' Processing helix chain 'A' and resid 555 through 560 removed outlier: 3.505A pdb=" N SER A 560 " --> pdb=" O GLN A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 566 Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 22 through 40 Processing helix chain 'B' and resid 51 through 55 removed outlier: 4.036A pdb=" N GLU B 54 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR B 55 " --> pdb=" O ILE B 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 51 through 55' Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 183 through 186 Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 271 through 276 removed outlier: 3.507A pdb=" N PHE B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 566 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 22 through 39 Processing helix chain 'C' and resid 50 through 55 removed outlier: 3.907A pdb=" N GLU C 54 " --> pdb=" O GLN C 51 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR C 55 " --> pdb=" O ILE C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 188 removed outlier: 4.252A pdb=" N TYR C 188 " --> pdb=" O GLY C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 228 Processing helix chain 'C' and resid 271 through 278 removed outlier: 3.827A pdb=" N PHE C 275 " --> pdb=" O THR C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 426 removed outlier: 3.584A pdb=" N ASN C 425 " --> pdb=" O GLU C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 476 No H-bonds generated for 'chain 'C' and resid 474 through 476' Processing helix chain 'C' and resid 554 through 560 removed outlier: 3.641A pdb=" N CYS C 558 " --> pdb=" O PRO C 554 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C 560 " --> pdb=" O GLN C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 566 removed outlier: 3.797A pdb=" N TYR C 566 " --> pdb=" O ILE C 562 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 332 removed outlier: 3.693A pdb=" N ILE A 331 " --> pdb=" O GLY A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 204 removed outlier: 7.181A pdb=" N PHE A 193 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU A 202 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A 191 " --> pdb=" O GLU A 202 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN A 190 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU A 194 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 356 " --> pdb=" O GLU A 194 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 233 through 234 removed outlier: 3.548A pdb=" N SER A 313 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 241 through 242 removed outlier: 3.858A pdb=" N ARG A 307 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG A 308 " --> pdb=" O CYS C 314 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN C 315 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL C 232 " --> pdb=" O ASN C 315 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 433 through 441 removed outlier: 3.594A pdb=" N VAL A 438 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS A 440 " --> pdb=" O SER A 627 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AA7, first strand: chain 'A' and resid 494 through 495 Processing sheet with id=AA8, first strand: chain 'A' and resid 539 through 544 removed outlier: 6.009A pdb=" N ILE A 540 " --> pdb=" O ASP A 551 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASP A 551 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL A 542 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 547 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AB1, first strand: chain 'B' and resid 327 through 328 removed outlier: 3.659A pdb=" N LEU B 327 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 110 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS B 107 " --> pdb=" O GLU B 411 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 109 " --> pdb=" O ASN B 409 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASN B 409 " --> pdb=" O ILE B 109 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 157 through 158 Processing sheet with id=AB3, first strand: chain 'B' and resid 176 through 179 removed outlier: 3.914A pdb=" N LEU B 176 " --> pdb=" O PHE B 371 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR B 178 " --> pdb=" O ASN B 369 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN B 369 " --> pdb=" O TYR B 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 198 through 204 removed outlier: 7.058A pdb=" N PHE B 193 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLU B 202 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL B 191 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N SER B 204 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU B 189 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN B 190 " --> pdb=" O LYS B 360 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 194 " --> pdb=" O PHE B 356 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.817A pdb=" N VAL B 232 " --> pdb=" O ASN B 315 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN B 315 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 313 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C 307 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 241 " --> pdb=" O ARG C 307 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 467 through 472 removed outlier: 3.535A pdb=" N PHE B 467 " --> pdb=" O SER B 626 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 504 through 505 Processing sheet with id=AB8, first strand: chain 'B' and resid 547 through 550 removed outlier: 3.892A pdb=" N ILE B 547 " --> pdb=" O ALA B 544 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL B 542 " --> pdb=" O LEU B 549 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 70 through 71 removed outlier: 3.538A pdb=" N GLY C 71 " --> pdb=" O PHE C 418 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 109 through 110 removed outlier: 3.717A pdb=" N LEU C 110 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 327 " --> pdb=" O LEU C 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.963A pdb=" N LEU C 176 " --> pdb=" O PHE C 371 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR C 178 " --> pdb=" O ASN C 369 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN C 369 " --> pdb=" O TYR C 178 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 198 through 204 removed outlier: 6.961A pdb=" N PHE C 193 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU C 202 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL C 191 " --> pdb=" O GLU C 202 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN C 190 " --> pdb=" O LYS C 360 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 434 through 436 removed outlier: 3.728A pdb=" N SER C 434 " --> pdb=" O LEU C 633 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 633 " --> pdb=" O SER C 434 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 444 through 446 removed outlier: 3.569A pdb=" N THR C 446 " --> pdb=" O ALA C 621 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA C 621 " --> pdb=" O THR C 446 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 580 through 582 removed outlier: 3.777A pdb=" N MET C 580 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE C 468 " --> pdb=" O MET C 580 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE C 582 " --> pdb=" O MET C 466 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER C 628 " --> pdb=" O GLU C 464 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 492 through 494 removed outlier: 3.574A pdb=" N HIS C 492 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU C 534 " --> pdb=" O HIS C 492 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 494 " --> pdb=" O ILE C 532 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 541 through 543 173 hydrogen bonds defined for protein. 426 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: 1.79 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3389 1.33 - 1.45: 2789 1.45 - 1.57: 7754 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 14002 Sorted by residual: bond pdb=" N ILE A 402 " pdb=" CA ILE A 402 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.12e+00 bond pdb=" N VAL A 401 " pdb=" CA VAL A 401 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.99e+00 bond pdb=" N ASN A 403 " pdb=" CA ASN A 403 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.32e-02 5.74e+03 6.10e+00 bond pdb=" N GLU A 404 " pdb=" CA GLU A 404 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.16e-02 7.43e+03 5.64e+00 bond pdb=" N ILE A 398 " pdb=" CA ILE A 398 " ideal model delta sigma weight residual 1.468 1.492 -0.024 1.05e-02 9.07e+03 5.26e+00 ... (remaining 13997 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 18841 1.82 - 3.63: 356 3.63 - 5.45: 45 5.45 - 7.26: 8 7.26 - 9.08: 2 Bond angle restraints: 19252 Sorted by residual: angle pdb=" N PRO A 399 " pdb=" CA PRO A 399 " pdb=" C PRO A 399 " ideal model delta sigma weight residual 111.33 120.41 -9.08 1.43e+00 4.89e-01 4.03e+01 angle pdb=" N ILE A 398 " pdb=" CA ILE A 398 " pdb=" C ILE A 398 " ideal model delta sigma weight residual 109.02 103.28 5.74 9.30e-01 1.16e+00 3.81e+01 angle pdb=" N PHE B 397 " pdb=" CA PHE B 397 " pdb=" C PHE B 397 " ideal model delta sigma weight residual 108.38 113.65 -5.27 1.35e+00 5.49e-01 1.52e+01 angle pdb=" CA PHE A 397 " pdb=" C PHE A 397 " pdb=" O PHE A 397 " ideal model delta sigma weight residual 122.13 117.78 4.35 1.13e+00 7.83e-01 1.48e+01 angle pdb=" C THR C 271 " pdb=" N ASN C 272 " pdb=" CA ASN C 272 " ideal model delta sigma weight residual 121.62 127.55 -5.93 1.57e+00 4.06e-01 1.43e+01 ... (remaining 19247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 7408 15.63 - 31.27: 623 31.27 - 46.90: 129 46.90 - 62.54: 12 62.54 - 78.17: 9 Dihedral angle restraints: 8181 sinusoidal: 2676 harmonic: 5505 Sorted by residual: dihedral pdb=" CA PHE A 283 " pdb=" C PHE A 283 " pdb=" N PRO A 284 " pdb=" CA PRO A 284 " ideal model delta harmonic sigma weight residual 180.00 154.95 25.05 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA PHE B 283 " pdb=" C PHE B 283 " pdb=" N PRO B 284 " pdb=" CA PRO B 284 " ideal model delta harmonic sigma weight residual 180.00 156.15 23.85 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA PRO A 84 " pdb=" C PRO A 84 " pdb=" N THR A 85 " pdb=" CA THR A 85 " ideal model delta harmonic sigma weight residual 180.00 -158.94 -21.06 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 8178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1854 0.063 - 0.125: 349 0.125 - 0.188: 18 0.188 - 0.251: 1 0.251 - 0.314: 1 Chirality restraints: 2223 Sorted by residual: chirality pdb=" CA ILE A 398 " pdb=" N ILE A 398 " pdb=" C ILE A 398 " pdb=" CB ILE A 398 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA PRO A 399 " pdb=" N PRO A 399 " pdb=" C PRO A 399 " pdb=" CB PRO A 399 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ILE A 522 " pdb=" N ILE A 522 " pdb=" C ILE A 522 " pdb=" CB ILE A 522 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.98e-01 ... (remaining 2220 not shown) Planarity restraints: 2509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 83 " 0.039 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO A 84 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 84 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 84 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 83 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO B 84 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 84 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 84 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 83 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO C 84 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 84 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 84 " 0.024 5.00e-02 4.00e+02 ... (remaining 2506 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2001 2.76 - 3.29: 13040 3.29 - 3.83: 19903 3.83 - 4.36: 21241 4.36 - 4.90: 38252 Nonbonded interactions: 94437 Sorted by model distance: nonbonded pdb=" OG SER C 116 " pdb=" O GLY C 400 " model vdw 2.222 3.040 nonbonded pdb=" OG1 THR A 446 " pdb=" O ALA A 621 " model vdw 2.226 3.040 nonbonded pdb=" O LYS B 460 " pdb=" OG SER B 601 " model vdw 2.231 3.040 nonbonded pdb=" OG SER B 116 " pdb=" O GLY B 400 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR C 446 " pdb=" O ALA C 621 " model vdw 2.256 3.040 ... (remaining 94432 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 8 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 41 or (resid 42 and (name N or name \ CA or name C or name O or name CB )) or resid 43 through 98 or (resid 99 and (n \ ame N or name CA or name C or name O or name CB )) or resid 100 through 132 or ( \ resid 133 through 135 and (name N or name CA or name C or name O or name CB )) o \ r resid 136 through 157 or (resid 158 and (name N or name CA or name C or name O \ or name CB )) or resid 160 through 184 or (resid 185 and (name N or name CA or \ name C or name O or name CB )) or resid 186 through 229 or (resid 230 through 23 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 232 through \ 248 or (resid 249 through 257 and (name N or name CA or name C or name O or name \ CB )) or resid 258 through 277 or (resid 278 and (name N or name CA or name C o \ r name O or name CB )) or resid 279 through 281 or (resid 282 and (name N or nam \ e CA or name C or name O or name CB )) or resid 284 or (resid 285 and (name N or \ name CA or name C or name O or name CB )) or resid 286 through 301 or (resid 30 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 303 through \ 317 or (resid 318 and (name N or name CA or name C or name O or name CB )) or re \ sid 319 through 341 or resid 344 through 364 or (resid 365 through 366 and (name \ N or name CA or name C or name O or name CB )) or resid 367 through 406 or (res \ id 407 through 408 and (name N or name CA or name C or name O or name CB )) or r \ esid 409 through 410 or (resid 411 and (name N or name CA or name C or name O or \ name CB )) or resid 412 through 476 or (resid 477 through 478 and (name N or na \ me CA or name C or name O or name CB )) or resid 479 through 484 or (resid 485 a \ nd (name N or name CA or name C or name O or name CB )) or resid 486 through 497 \ or (resid 498 and (name N or name CA or name C or name O or name CB )) or resid \ 499 through 509 or (resid 510 and (name N or name CA or name C or name O or nam \ e CB )) or resid 511 through 520 or (resid 521 and (name N or name CA or name C \ or name O or name CB )) or resid 522 through 540 or (resid 541 and (name N or na \ me CA or name C or name O or name CB )) or resid 542 through 550 or (resid 551 a \ nd (name N or name CA or name C or name O or name CB )) or resid 552 through 574 \ or (resid 575 through 576 and (name N or name CA or name C or name O or name CB \ )) or resid 577 through 618 or (resid 619 and (name N or name CA or name C or n \ ame O or name CB )) or resid 620 through 626 or (resid 627 and (name N or name C \ A or name C or name O or name CB )) or resid 628 through 636)) selection = (chain 'B' and (resid 8 through 16 or (resid 17 through 18 and (name N or name C \ A or name C or name O or name CB )) or resid 19 through 29 or (resid 30 through \ 32 and (name N or name CA or name C or name O or name CB )) or resid 33 or (resi \ d 34 and (name N or name CA or name C or name O or name CB )) or resid 35 or (re \ sid 36 and (name N or name CA or name C or name O or name CB )) or resid 37 thro \ ugh 38 or (resid 39 and (name N or name CA or name C or name O or name CB )) or \ resid 40 through 47 or (resid 48 through 49 and (name N or name CA or name C or \ name O or name CB )) or resid 50 through 51 or (resid 52 and (name N or name CA \ or name C or name O or name CB )) or resid 53 through 54 or (resid 55 and (name \ N or name CA or name C or name O or name CB )) or resid 56 through 62 or (resid \ 63 and (name N or name CA or name C or name O or name CB )) or resid 64 through \ 85 or (resid 86 and (name N or name CA or name C or name O or name CB )) or resi \ d 87 through 93 or (resid 94 and (name N or name CA or name C or name O or name \ CB )) or resid 95 through 103 or (resid 104 and (name N or name CA or name C or \ name O or name CB )) or resid 105 through 122 or (resid 123 and (name N or name \ CA or name C or name O or name CB )) or resid 124 through 144 or (resid 145 and \ (name N or name CA or name C or name O or name CB )) or resid 146 through 158 or \ (resid 160 through 161 and (name N or name CA or name C or name O or name CB )) \ or resid 162 through 184 or (resid 185 and (name N or name CA or name C or name \ O or name CB )) or resid 186 through 218 or (resid 219 and (name N or name CA o \ r name C or name O or name CB )) or resid 220 through 229 or (resid 230 through \ 231 and (name N or name CA or name C or name O or name CB )) or resid 232 throug \ h 234 or (resid 235 and (name N or name CA or name C or name O or name CB )) or \ resid 236 through 248 or (resid 249 through 257 and (name N or name CA or name C \ or name O or name CB )) or resid 258 or (resid 259 through 260 and (name N or n \ ame CA or name C or name O or name CB )) or resid 261 through 275 or (resid 276 \ and (name N or name CA or name C or name O or name CB )) or resid 277 or (resid \ 278 and (name N or name CA or name C or name O or name CB )) or resid 279 throug \ h 282 or resid 284 through 294 or (resid 295 and (name N or name CA or name C or \ name O or name CB )) or resid 296 or (resid 297 and (name N or name CA or name \ C or name O or name CB )) or resid 298 through 301 or (resid 302 and (name N or \ name CA or name C or name O or name CB )) or resid 303 or (resid 304 through 305 \ and (name N or name CA or name C or name O or name CB )) or resid 306 through 3 \ 41 or resid 344 through 362 or (resid 363 through 366 and (name N or name CA or \ name C or name O or name CB )) or resid 367 through 410 or (resid 411 and (name \ N or name CA or name C or name O or name CB )) or resid 412 through 428 or (resi \ d 429 through 430 and (name N or name CA or name C or name O or name CB )) or re \ sid 431 through 477 or (resid 478 and (name N or name CA or name C or name O or \ name CB )) or resid 479 through 484 or (resid 485 and (name N or name CA or name \ C or name O or name CB )) or resid 486 through 497 or (resid 498 and (name N or \ name CA or name C or name O or name CB )) or resid 499 through 509 or (resid 51 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 511 through \ 516 or (resid 517 through 518 and (name N or name CA or name C or name O or name \ CB )) or resid 519 through 540 or (resid 541 and (name N or name CA or name C o \ r name O or name CB )) or resid 542 through 550 or (resid 551 and (name N or nam \ e CA or name C or name O or name CB )) or resid 552 through 554 or (resid 555 an \ d (name N or name CA or name C or name O or name CB )) or resid 556 through 574 \ or (resid 575 through 576 and (name N or name CA or name C or name O or name CB \ )) or resid 577 through 592 or (resid 593 and (name N or name CA or name C or na \ me O or name CB )) or resid 594 through 636)) selection = (chain 'C' and (resid 8 through 29 or (resid 30 through 32 and (name N or name C \ A or name C or name O or name CB )) or resid 33 or (resid 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 or (resid 36 and (name N or na \ me 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 47 or ( \ resid 48 through 49 and (name N or name CA or name C or name O or name CB )) or \ resid 50 or (resid 51 through 52 and (name N or name CA or name C or name O or n \ ame CB )) or resid 53 through 54 or (resid 55 and (name N or name CA or name C o \ r name O or name CB )) or resid 56 through 62 or (resid 63 and (name N or name C \ A or name C or name O or name CB )) or resid 64 through 85 or (resid 86 and (nam \ e N or name CA or name C or name O or name CB )) or resid 87 through 93 or (resi \ d 94 and (name N or name CA or name C or name O or name CB )) or resid 95 throug \ h 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 103 or (resid 104 and (name N or name CA or name C or name O or \ name CB )) or resid 105 through 122 or (resid 123 and (name N or name CA or name \ C or name O or name CB )) or resid 124 through 132 or (resid 133 through 135 an \ d (name N or name CA or name C or name O or name CB )) or resid 136 through 158 \ or (resid 160 through 161 and (name N or name CA or name C or name O or name CB \ )) or resid 162 through 205 or (resid 206 and (name N or name CA or name C or na \ me O or name CB )) or resid 207 through 218 or (resid 219 and (name N or name CA \ or name C or name O or name CB )) or resid 220 through 234 or (resid 235 and (n \ ame N or name CA or name C or name O or name CB )) or resid 236 through 258 or ( \ resid 259 through 260 and (name N or name CA or name C or name O or name CB )) o \ r resid 261 through 281 or (resid 282 and (name N or name CA or name C or name O \ or name CB )) or resid 284 or (resid 285 and (name N or name CA or name C or na \ me O or name CB )) or resid 286 through 294 or (resid 295 and (name N or name CA \ or name C or name O or name CB )) or resid 296 or (resid 297 and (name N or nam \ e CA or name C or name O or name CB )) or resid 298 through 317 or (resid 318 an \ d (name N or name CA or name C or name O or name CB )) or resid 319 through 341 \ or resid 344 through 362 or (resid 363 through 366 and (name N or name CA or nam \ e C or name O or name CB )) or resid 367 through 407 or (resid 408 and (name N o \ r name CA or name C or name O or name CB )) or resid 409 through 476 or (resid 4 \ 77 through 478 and (name N or name CA or name C or name O or name CB )) or resid \ 479 through 516 or (resid 517 through 518 and (name N or name CA or name C or n \ ame O or name CB )) or resid 519 through 520 or (resid 521 and (name N or name C \ A or name C or name O or name CB )) or resid 522 through 554 or (resid 555 and ( \ name N or name CA or name C or name O or name CB )) or resid 556 through 592 or \ (resid 593 and (name N or name CA or name C or name O or name CB )) or resid 594 \ through 617 or (resid 618 through 619 and (name N or name CA or name C or name \ O or name CB )) or resid 620 through 626 or (resid 627 and (name N or name CA or \ name C or name O or name CB )) or resid 628 through 636)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 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: 0.050 Set scattering table: 0.030 Process input model: 12.840 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14002 Z= 0.143 Angle : 0.606 9.077 19252 Z= 0.334 Chirality : 0.047 0.314 2223 Planarity : 0.005 0.060 2509 Dihedral : 12.334 78.173 4629 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.83 % Favored : 86.01 % Rotamer: Outliers : 0.15 % Allowed : 8.75 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.72 (0.15), residues: 1873 helix: -1.79 (0.40), residues: 141 sheet: -3.78 (0.19), residues: 461 loop : -4.35 (0.13), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 192 TYR 0.015 0.001 TYR B 465 PHE 0.024 0.001 PHE A 467 TRP 0.007 0.001 TRP B 474 HIS 0.005 0.001 HIS C 131 Details of bonding type rmsd covalent geometry : bond 0.00284 (14002) covalent geometry : angle 0.60567 (19252) hydrogen bonds : bond 0.26435 ( 173) hydrogen bonds : angle 9.41421 ( 426) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 324 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ARG cc_start: 0.7589 (ttt-90) cc_final: 0.7302 (ttt-90) REVERT: A 179 TYR cc_start: 0.8777 (m-10) cc_final: 0.8575 (m-10) REVERT: A 315 ASN cc_start: 0.8087 (t0) cc_final: 0.6873 (p0) REVERT: A 416 ASN cc_start: 0.9184 (m-40) cc_final: 0.8949 (m-40) REVERT: A 461 TRP cc_start: 0.8101 (m-90) cc_final: 0.7676 (m100) REVERT: B 78 ARG cc_start: 0.5631 (mtt180) cc_final: 0.5388 (mtt180) REVERT: B 220 LYS cc_start: 0.8361 (mppt) cc_final: 0.8083 (mttt) REVERT: B 356 PHE cc_start: 0.7970 (m-80) cc_final: 0.7753 (m-80) REVERT: B 498 MET cc_start: 0.8148 (mtp) cc_final: 0.7398 (mtp) REVERT: B 530 TYR cc_start: 0.8624 (m-80) cc_final: 0.7573 (m-80) REVERT: C 60 PHE cc_start: 0.7466 (p90) cc_final: 0.7223 (p90) REVERT: C 182 TYR cc_start: 0.8385 (m-80) cc_final: 0.8053 (m-80) REVERT: C 440 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8318 (mmmt) REVERT: C 505 GLU cc_start: 0.7086 (tm-30) cc_final: 0.5173 (mp0) outliers start: 2 outliers final: 2 residues processed: 326 average time/residue: 0.1168 time to fit residues: 54.8017 Evaluate side-chains 247 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 245 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.0870 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.0010 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.0670 overall best weight: 0.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 HIS A 107 HIS A 282 HIS A 311 HIS A 445 HIS A 483 GLN B 147 GLN B 226 HIS B 410 ASN ** B 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS C 539 ASN C 597 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.181496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.166883 restraints weight = 17311.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.160252 restraints weight = 21310.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.158248 restraints weight = 18295.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.158484 restraints weight = 17336.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.158554 restraints weight = 16036.597| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14002 Z= 0.106 Angle : 0.601 6.911 19252 Z= 0.302 Chirality : 0.046 0.171 2223 Planarity : 0.005 0.085 2509 Dihedral : 4.376 23.405 1985 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.95 % Favored : 89.00 % Rotamer: Outliers : 0.08 % Allowed : 4.10 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.85 (0.17), residues: 1873 helix: -1.13 (0.42), residues: 143 sheet: -3.38 (0.21), residues: 440 loop : -3.67 (0.15), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 192 TYR 0.018 0.001 TYR C 465 PHE 0.016 0.001 PHE A 467 TRP 0.013 0.001 TRP C 474 HIS 0.007 0.001 HIS C 131 Details of bonding type rmsd covalent geometry : bond 0.00234 (14002) covalent geometry : angle 0.60080 (19252) hydrogen bonds : bond 0.03521 ( 173) hydrogen bonds : angle 6.49118 ( 426) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 289 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 TYR cc_start: 0.8797 (m-10) cc_final: 0.8553 (m-10) REVERT: A 315 ASN cc_start: 0.8093 (t0) cc_final: 0.6944 (p0) REVERT: A 386 PRO cc_start: 0.7624 (Cg_exo) cc_final: 0.7341 (Cg_endo) REVERT: A 416 ASN cc_start: 0.9153 (m-40) cc_final: 0.8939 (m-40) REVERT: A 461 TRP cc_start: 0.8202 (m-90) cc_final: 0.7648 (m100) REVERT: B 78 ARG cc_start: 0.5305 (mtt180) cc_final: 0.4785 (mmt90) REVERT: B 182 TYR cc_start: 0.8180 (m-80) cc_final: 0.7768 (m-80) REVERT: B 415 ASN cc_start: 0.8539 (p0) cc_final: 0.8190 (m-40) REVERT: B 416 ASN cc_start: 0.9027 (m-40) cc_final: 0.8730 (m-40) REVERT: B 498 MET cc_start: 0.8088 (mtp) cc_final: 0.7367 (mtp) REVERT: B 530 TYR cc_start: 0.8572 (m-80) cc_final: 0.7412 (m-80) REVERT: C 27 ASN cc_start: 0.7663 (m110) cc_final: 0.7126 (m110) REVERT: C 60 PHE cc_start: 0.7496 (p90) cc_final: 0.7288 (p90) REVERT: C 182 TYR cc_start: 0.8266 (m-80) cc_final: 0.8003 (m-80) REVERT: C 440 LYS cc_start: 0.8475 (mmtt) cc_final: 0.8178 (mmmt) REVERT: C 505 GLU cc_start: 0.6925 (tm-30) cc_final: 0.5227 (mp0) outliers start: 1 outliers final: 0 residues processed: 289 average time/residue: 0.0980 time to fit residues: 42.3567 Evaluate side-chains 235 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 165 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 116 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 147 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 180 optimal weight: 0.0970 chunk 63 optimal weight: 5.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 311 HIS A 445 HIS B 503 HIS B 565 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.179564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.170538 restraints weight = 17452.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.156956 restraints weight = 23848.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.156813 restraints weight = 22037.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.156786 restraints weight = 20203.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.156774 restraints weight = 18379.780| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14002 Z= 0.123 Angle : 0.603 7.286 19252 Z= 0.303 Chirality : 0.046 0.167 2223 Planarity : 0.005 0.097 2509 Dihedral : 4.510 24.357 1985 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.81 % Favored : 87.13 % Rotamer: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.55 (0.17), residues: 1873 helix: -0.82 (0.44), residues: 143 sheet: -3.05 (0.21), residues: 462 loop : -3.50 (0.16), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 192 TYR 0.023 0.002 TYR B 413 PHE 0.016 0.001 PHE A 92 TRP 0.015 0.001 TRP B 474 HIS 0.004 0.001 HIS C 108 Details of bonding type rmsd covalent geometry : bond 0.00288 (14002) covalent geometry : angle 0.60304 (19252) hydrogen bonds : bond 0.03302 ( 173) hydrogen bonds : angle 5.80882 ( 426) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 TYR cc_start: 0.8794 (m-10) cc_final: 0.8569 (m-10) REVERT: A 315 ASN cc_start: 0.8019 (t0) cc_final: 0.6800 (p0) REVERT: A 386 PRO cc_start: 0.7666 (Cg_exo) cc_final: 0.7421 (Cg_endo) REVERT: A 416 ASN cc_start: 0.9317 (m-40) cc_final: 0.9105 (m-40) REVERT: A 461 TRP cc_start: 0.8217 (m-90) cc_final: 0.7655 (m100) REVERT: B 78 ARG cc_start: 0.5469 (mtt180) cc_final: 0.5092 (mtt180) REVERT: B 415 ASN cc_start: 0.8736 (p0) cc_final: 0.8098 (m-40) REVERT: B 416 ASN cc_start: 0.9119 (m-40) cc_final: 0.8734 (m-40) REVERT: B 498 MET cc_start: 0.8234 (mtp) cc_final: 0.7357 (mtp) REVERT: B 530 TYR cc_start: 0.8469 (m-80) cc_final: 0.7478 (m-80) REVERT: C 27 ASN cc_start: 0.7784 (m110) cc_final: 0.7279 (m110) REVERT: C 60 PHE cc_start: 0.7740 (p90) cc_final: 0.7525 (p90) REVERT: C 182 TYR cc_start: 0.8375 (m-80) cc_final: 0.7998 (m-80) REVERT: C 440 LYS cc_start: 0.8478 (mmtt) cc_final: 0.8150 (mmmt) REVERT: C 456 MET cc_start: 0.7238 (tpt) cc_final: 0.6801 (tpp) REVERT: C 505 GLU cc_start: 0.6875 (tm-30) cc_final: 0.5005 (mp0) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.0984 time to fit residues: 42.0048 Evaluate side-chains 217 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 5 optimal weight: 0.5980 chunk 182 optimal weight: 0.0980 chunk 32 optimal weight: 0.4980 chunk 57 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 55 optimal weight: 0.2980 chunk 98 optimal weight: 0.3980 chunk 68 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS A 445 HIS ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 ASN B 548 ASN C 445 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.183772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.173865 restraints weight = 17179.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.161491 restraints weight = 25089.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.161155 restraints weight = 21481.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.161352 restraints weight = 19164.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.161730 restraints weight = 16550.605| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14002 Z= 0.094 Angle : 0.581 7.345 19252 Z= 0.290 Chirality : 0.046 0.166 2223 Planarity : 0.005 0.093 2509 Dihedral : 4.268 22.397 1985 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.68 % Favored : 89.27 % Rotamer: Outliers : 0.08 % Allowed : 2.79 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.12 (0.18), residues: 1873 helix: -0.64 (0.44), residues: 143 sheet: -2.64 (0.22), residues: 452 loop : -3.25 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 163 TYR 0.018 0.001 TYR C 323 PHE 0.025 0.001 PHE A 60 TRP 0.017 0.001 TRP C 474 HIS 0.004 0.000 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00221 (14002) covalent geometry : angle 0.58093 (19252) hydrogen bonds : bond 0.02568 ( 173) hydrogen bonds : angle 5.43672 ( 426) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 290 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.4201 (mtt180) cc_final: 0.3985 (mtt180) REVERT: A 179 TYR cc_start: 0.8772 (m-10) cc_final: 0.8489 (m-10) REVERT: A 315 ASN cc_start: 0.7739 (t0) cc_final: 0.6516 (p0) REVERT: A 386 PRO cc_start: 0.7577 (Cg_exo) cc_final: 0.7350 (Cg_endo) REVERT: A 461 TRP cc_start: 0.8106 (m-90) cc_final: 0.7627 (m100) REVERT: A 475 ASN cc_start: 0.7617 (m-40) cc_final: 0.7367 (m-40) REVERT: A 530 TYR cc_start: 0.8405 (m-80) cc_final: 0.7409 (m-80) REVERT: B 78 ARG cc_start: 0.5186 (mtt180) cc_final: 0.4694 (mmt90) REVERT: B 221 MET cc_start: 0.6893 (tpp) cc_final: 0.6640 (tpp) REVERT: B 411 GLU cc_start: 0.8022 (mp0) cc_final: 0.7564 (mp0) REVERT: B 415 ASN cc_start: 0.8666 (p0) cc_final: 0.8091 (m110) REVERT: B 416 ASN cc_start: 0.8947 (m-40) cc_final: 0.8729 (m-40) REVERT: B 498 MET cc_start: 0.8001 (mtp) cc_final: 0.7278 (mtp) REVERT: B 530 TYR cc_start: 0.8500 (m-80) cc_final: 0.7444 (m-80) REVERT: C 27 ASN cc_start: 0.7590 (m110) cc_final: 0.7112 (m110) REVERT: C 72 PHE cc_start: 0.8053 (p90) cc_final: 0.7661 (p90) REVERT: C 204 SER cc_start: 0.9078 (m) cc_final: 0.8715 (t) REVERT: C 456 MET cc_start: 0.7200 (tpt) cc_final: 0.6920 (tpp) REVERT: C 505 GLU cc_start: 0.6720 (tm-30) cc_final: 0.5216 (mp0) REVERT: C 608 ILE cc_start: 0.8678 (mt) cc_final: 0.8461 (mt) outliers start: 1 outliers final: 0 residues processed: 291 average time/residue: 0.1014 time to fit residues: 44.7915 Evaluate side-chains 225 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 133 optimal weight: 0.0050 chunk 17 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 175 optimal weight: 30.0000 chunk 74 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 138 optimal weight: 0.0980 chunk 49 optimal weight: 7.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 311 HIS ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 HIS ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 HIS B 475 ASN B 548 ASN C 226 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.178812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.163568 restraints weight = 17603.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.156335 restraints weight = 22075.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.154925 restraints weight = 19450.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.155255 restraints weight = 18618.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.155615 restraints weight = 15505.084| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14002 Z= 0.139 Angle : 0.614 7.625 19252 Z= 0.308 Chirality : 0.047 0.187 2223 Planarity : 0.006 0.108 2509 Dihedral : 4.509 25.288 1985 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.92 % Favored : 87.03 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.12 (0.18), residues: 1873 helix: -0.51 (0.45), residues: 143 sheet: -2.46 (0.21), residues: 502 loop : -3.34 (0.16), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 307 TYR 0.020 0.002 TYR A 178 PHE 0.018 0.001 PHE A 60 TRP 0.016 0.001 TRP C 474 HIS 0.005 0.001 HIS C 226 Details of bonding type rmsd covalent geometry : bond 0.00323 (14002) covalent geometry : angle 0.61381 (19252) hydrogen bonds : bond 0.02930 ( 173) hydrogen bonds : angle 5.32897 ( 426) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 PRO cc_start: 0.7670 (Cg_exo) cc_final: 0.7453 (Cg_endo) REVERT: A 461 TRP cc_start: 0.8157 (m-90) cc_final: 0.7632 (m100) REVERT: A 475 ASN cc_start: 0.7378 (m-40) cc_final: 0.7123 (m-40) REVERT: B 78 ARG cc_start: 0.5384 (mtt180) cc_final: 0.5017 (mtt180) REVERT: B 221 MET cc_start: 0.7069 (tpp) cc_final: 0.6868 (tpp) REVERT: B 415 ASN cc_start: 0.8790 (p0) cc_final: 0.8055 (m110) REVERT: B 416 ASN cc_start: 0.9008 (m-40) cc_final: 0.8796 (m-40) REVERT: C 27 ASN cc_start: 0.7737 (m110) cc_final: 0.7328 (m110) REVERT: C 72 PHE cc_start: 0.8118 (p90) cc_final: 0.7715 (p90) REVERT: C 199 SER cc_start: 0.8946 (t) cc_final: 0.8519 (p) REVERT: C 440 LYS cc_start: 0.8516 (mmtt) cc_final: 0.8145 (mmmt) REVERT: C 456 MET cc_start: 0.7165 (tpt) cc_final: 0.6877 (tpp) REVERT: C 505 GLU cc_start: 0.6791 (tm-30) cc_final: 0.5198 (mp0) REVERT: C 584 PHE cc_start: 0.8460 (m-80) cc_final: 0.8206 (m-10) REVERT: C 608 ILE cc_start: 0.8741 (mt) cc_final: 0.8515 (mt) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.0973 time to fit residues: 41.4186 Evaluate side-chains 209 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 2 optimal weight: 3.9990 chunk 143 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 59 optimal weight: 0.0020 chunk 173 optimal weight: 5.9990 overall best weight: 2.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS ** C 318 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 = 0.3914 r_free = 0.3914 target = 0.174861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.159724 restraints weight = 17776.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.152326 restraints weight = 23199.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.150783 restraints weight = 19236.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.151151 restraints weight = 20024.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.151302 restraints weight = 17050.701| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14002 Z= 0.171 Angle : 0.662 9.272 19252 Z= 0.334 Chirality : 0.049 0.210 2223 Planarity : 0.006 0.104 2509 Dihedral : 4.910 24.120 1985 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 14.79 % Favored : 85.16 % Rotamer: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.22 (0.18), residues: 1873 helix: -0.62 (0.44), residues: 143 sheet: -2.58 (0.22), residues: 504 loop : -3.39 (0.16), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 192 TYR 0.020 0.002 TYR B 188 PHE 0.019 0.002 PHE A 584 TRP 0.019 0.001 TRP C 474 HIS 0.009 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00397 (14002) covalent geometry : angle 0.66201 (19252) hydrogen bonds : bond 0.03106 ( 173) hydrogen bonds : angle 5.45352 ( 426) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 TYR cc_start: 0.8735 (m-10) cc_final: 0.8234 (m-10) REVERT: A 386 PRO cc_start: 0.7757 (Cg_exo) cc_final: 0.7554 (Cg_endo) REVERT: A 461 TRP cc_start: 0.8313 (m-90) cc_final: 0.7654 (m100) REVERT: B 50 SER cc_start: 0.7279 (p) cc_final: 0.7037 (m) REVERT: B 78 ARG cc_start: 0.5665 (mtt180) cc_final: 0.5381 (mtt180) REVERT: B 498 MET cc_start: 0.7958 (mtp) cc_final: 0.7177 (mtp) REVERT: B 530 TYR cc_start: 0.8531 (m-80) cc_final: 0.7899 (m-80) REVERT: C 27 ASN cc_start: 0.7803 (m110) cc_final: 0.7344 (m110) REVERT: C 199 SER cc_start: 0.8809 (t) cc_final: 0.8316 (p) REVERT: C 440 LYS cc_start: 0.8605 (mmtt) cc_final: 0.8198 (mmmt) REVERT: C 505 GLU cc_start: 0.6979 (tm-30) cc_final: 0.5458 (mp0) REVERT: C 530 TYR cc_start: 0.8584 (m-80) cc_final: 0.8276 (m-80) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.0999 time to fit residues: 42.8807 Evaluate side-chains 220 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 172 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN B 445 HIS B 483 GLN B 503 HIS B 548 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.180976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.170938 restraints weight = 17543.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.158167 restraints weight = 26344.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.157526 restraints weight = 24744.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.157831 restraints weight = 22196.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.158493 restraints weight = 17778.522| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14002 Z= 0.103 Angle : 0.607 7.619 19252 Z= 0.304 Chirality : 0.046 0.171 2223 Planarity : 0.006 0.113 2509 Dihedral : 4.560 24.353 1985 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.16 % Favored : 88.79 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.99 (0.18), residues: 1873 helix: -0.39 (0.45), residues: 143 sheet: -2.50 (0.21), residues: 522 loop : -3.18 (0.16), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 192 TYR 0.017 0.001 TYR C 465 PHE 0.020 0.001 PHE A 137 TRP 0.020 0.001 TRP C 474 HIS 0.007 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00242 (14002) covalent geometry : angle 0.60733 (19252) hydrogen bonds : bond 0.02489 ( 173) hydrogen bonds : angle 5.23625 ( 426) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 TYR cc_start: 0.8681 (m-10) cc_final: 0.8296 (m-10) REVERT: A 368 VAL cc_start: 0.9315 (t) cc_final: 0.9096 (p) REVERT: A 386 PRO cc_start: 0.7631 (Cg_exo) cc_final: 0.7413 (Cg_endo) REVERT: A 461 TRP cc_start: 0.8182 (m-90) cc_final: 0.7701 (m100) REVERT: B 53 GLU cc_start: 0.6302 (mp0) cc_final: 0.6035 (mp0) REVERT: B 78 ARG cc_start: 0.5308 (mtt180) cc_final: 0.4980 (mtt180) REVERT: B 498 MET cc_start: 0.8027 (mtp) cc_final: 0.7133 (mtp) REVERT: B 530 TYR cc_start: 0.8440 (m-80) cc_final: 0.7590 (m-80) REVERT: C 27 ASN cc_start: 0.7728 (m110) cc_final: 0.7328 (m110) REVERT: C 440 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8261 (mmmt) REVERT: C 505 GLU cc_start: 0.6876 (tm-30) cc_final: 0.5570 (mp0) REVERT: C 530 TYR cc_start: 0.8322 (m-80) cc_final: 0.8012 (m-80) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.0949 time to fit residues: 38.4668 Evaluate side-chains 215 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 25 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 174 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 143 optimal weight: 0.0970 chunk 116 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 178 optimal weight: 0.5980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 HIS B 548 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.181985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.172819 restraints weight = 17024.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.159773 restraints weight = 23050.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.160029 restraints weight = 19450.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.159983 restraints weight = 17682.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.159921 restraints weight = 18977.720| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14002 Z= 0.100 Angle : 0.604 7.588 19252 Z= 0.301 Chirality : 0.046 0.213 2223 Planarity : 0.006 0.113 2509 Dihedral : 4.400 23.437 1985 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.80 % Favored : 88.15 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.76 (0.18), residues: 1873 helix: -0.33 (0.45), residues: 143 sheet: -2.28 (0.22), residues: 506 loop : -3.04 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 192 TYR 0.017 0.001 TYR B 465 PHE 0.019 0.001 PHE A 137 TRP 0.016 0.001 TRP C 474 HIS 0.005 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00235 (14002) covalent geometry : angle 0.60352 (19252) hydrogen bonds : bond 0.02420 ( 173) hydrogen bonds : angle 5.09799 ( 426) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 TYR cc_start: 0.8635 (m-10) cc_final: 0.8313 (m-10) REVERT: A 386 PRO cc_start: 0.7625 (Cg_exo) cc_final: 0.7391 (Cg_endo) REVERT: A 461 TRP cc_start: 0.8169 (m-90) cc_final: 0.7713 (m100) REVERT: B 78 ARG cc_start: 0.5276 (mtt180) cc_final: 0.4732 (mmt90) REVERT: B 411 GLU cc_start: 0.7948 (mp0) cc_final: 0.7639 (mp0) REVERT: B 605 GLU cc_start: 0.7332 (pm20) cc_final: 0.6874 (tp30) REVERT: C 27 ASN cc_start: 0.7714 (m110) cc_final: 0.7304 (m110) REVERT: C 440 LYS cc_start: 0.8579 (mmtt) cc_final: 0.8172 (mmmt) REVERT: C 463 ILE cc_start: 0.8992 (tt) cc_final: 0.8637 (tt) REVERT: C 505 GLU cc_start: 0.6800 (tm-30) cc_final: 0.5531 (mp0) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.0948 time to fit residues: 39.1343 Evaluate side-chains 214 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 51 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 140 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 112 optimal weight: 0.0060 chunk 159 optimal weight: 0.9980 chunk 158 optimal weight: 0.0170 chunk 40 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 50 optimal weight: 0.0470 overall best weight: 0.3332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 GLN B 445 HIS B 548 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.184734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.174769 restraints weight = 17113.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.162122 restraints weight = 24344.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.161694 restraints weight = 22371.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.161747 restraints weight = 21641.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.162089 restraints weight = 17645.884| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14002 Z= 0.096 Angle : 0.594 7.522 19252 Z= 0.296 Chirality : 0.045 0.197 2223 Planarity : 0.006 0.116 2509 Dihedral : 4.217 23.276 1985 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.84 % Favored : 89.11 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.18), residues: 1873 helix: -0.25 (0.45), residues: 143 sheet: -2.13 (0.22), residues: 501 loop : -2.89 (0.17), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 192 TYR 0.023 0.001 TYR B 465 PHE 0.019 0.001 PHE C 60 TRP 0.026 0.001 TRP C 474 HIS 0.005 0.000 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00224 (14002) covalent geometry : angle 0.59424 (19252) hydrogen bonds : bond 0.02165 ( 173) hydrogen bonds : angle 4.89341 ( 426) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 ARG cc_start: 0.6919 (ttt-90) cc_final: 0.5781 (ttm-80) REVERT: A 179 TYR cc_start: 0.8574 (m-10) cc_final: 0.8295 (m-10) REVERT: A 386 PRO cc_start: 0.7576 (Cg_exo) cc_final: 0.7374 (Cg_endo) REVERT: A 461 TRP cc_start: 0.8097 (m-90) cc_final: 0.7675 (m100) REVERT: B 78 ARG cc_start: 0.5309 (mtt180) cc_final: 0.4798 (mmt90) REVERT: B 411 GLU cc_start: 0.7964 (mp0) cc_final: 0.7506 (mp0) REVERT: B 530 TYR cc_start: 0.8288 (m-80) cc_final: 0.8074 (m-80) REVERT: C 27 ASN cc_start: 0.7650 (m110) cc_final: 0.7233 (m110) REVERT: C 72 PHE cc_start: 0.8126 (p90) cc_final: 0.7677 (p90) REVERT: C 463 ILE cc_start: 0.8869 (tt) cc_final: 0.8584 (tt) REVERT: C 505 GLU cc_start: 0.6760 (tm-30) cc_final: 0.5521 (mp0) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.0964 time to fit residues: 40.3929 Evaluate side-chains 224 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 138 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 12 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 94 optimal weight: 0.0970 chunk 133 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 128 optimal weight: 9.9990 chunk 181 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 ASN A 499 GLN B 445 HIS B 548 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.185064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.175602 restraints weight = 17078.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.161887 restraints weight = 24331.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.161878 restraints weight = 22118.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.162019 restraints weight = 19021.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.162139 restraints weight = 17347.457| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14002 Z= 0.096 Angle : 0.597 7.744 19252 Z= 0.297 Chirality : 0.045 0.194 2223 Planarity : 0.006 0.113 2509 Dihedral : 4.135 22.397 1985 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.05 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.19), residues: 1873 helix: -0.19 (0.46), residues: 143 sheet: -2.04 (0.22), residues: 515 loop : -2.84 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 192 TYR 0.022 0.001 TYR B 97 PHE 0.024 0.001 PHE B 72 TRP 0.020 0.001 TRP C 474 HIS 0.005 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00228 (14002) covalent geometry : angle 0.59727 (19252) hydrogen bonds : bond 0.02259 ( 173) hydrogen bonds : angle 4.93057 ( 426) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7998 (tm-30) REVERT: A 179 TYR cc_start: 0.8598 (m-10) cc_final: 0.8296 (m-10) REVERT: A 386 PRO cc_start: 0.7579 (Cg_exo) cc_final: 0.7379 (Cg_endo) REVERT: A 461 TRP cc_start: 0.8083 (m-90) cc_final: 0.7639 (m100) REVERT: B 78 ARG cc_start: 0.5318 (mtt180) cc_final: 0.4806 (mmt90) REVERT: B 411 GLU cc_start: 0.7983 (mp0) cc_final: 0.7520 (mp0) REVERT: B 530 TYR cc_start: 0.8229 (m-80) cc_final: 0.7701 (m-80) REVERT: B 605 GLU cc_start: 0.7128 (pm20) cc_final: 0.6734 (tp30) REVERT: C 27 ASN cc_start: 0.7698 (m110) cc_final: 0.7248 (m110) REVERT: C 72 PHE cc_start: 0.8104 (p90) cc_final: 0.7684 (p90) REVERT: C 505 GLU cc_start: 0.6721 (tm-30) cc_final: 0.5325 (mp0) REVERT: C 530 TYR cc_start: 0.8099 (m-80) cc_final: 0.7877 (m-80) REVERT: C 540 ILE cc_start: 0.8962 (mm) cc_final: 0.8762 (mm) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.0986 time to fit residues: 40.4443 Evaluate side-chains 222 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 173 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 GLN B 23 GLN B 445 HIS B 548 ASN C 424 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.176247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.166288 restraints weight = 17647.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.154417 restraints weight = 26930.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.153288 restraints weight = 25939.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.153911 restraints weight = 22793.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.154160 restraints weight = 20054.884| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14002 Z= 0.173 Angle : 0.672 7.910 19252 Z= 0.341 Chirality : 0.048 0.195 2223 Planarity : 0.006 0.122 2509 Dihedral : 4.846 24.741 1985 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 14.42 % Favored : 85.53 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.78 (0.18), residues: 1873 helix: -0.61 (0.43), residues: 155 sheet: -2.22 (0.22), residues: 516 loop : -3.08 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 192 TYR 0.032 0.002 TYR B 465 PHE 0.025 0.002 PHE A 137 TRP 0.020 0.002 TRP B 474 HIS 0.011 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00400 (14002) covalent geometry : angle 0.67239 (19252) hydrogen bonds : bond 0.02923 ( 173) hydrogen bonds : angle 5.21964 ( 426) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1913.56 seconds wall clock time: 33 minutes 49.39 seconds (2029.39 seconds total)