Starting phenix.real_space_refine on Thu Jul 31 10:54:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6l2t_0814/07_2025/6l2t_0814.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l2t_0814/07_2025/6l2t_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_0814/07_2025/6l2t_0814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l2t_0814/07_2025/6l2t_0814.map" model { file = "/net/cci-nas-00/data/ceres_data/6l2t_0814/07_2025/6l2t_0814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l2t_0814/07_2025/6l2t_0814.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 10, 'ASP:plan': 22, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'HIS:plan': 7, 'PHE:plan': 7, 'GLU:plan': 16, 'ARG:plan': 15} 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: {'GLN:plan1': 10, 'ASP:plan': 19, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 7, 'PHE:plan': 7, 'GLU:plan': 16, 'ARG:plan': 15} 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: {'GLN:plan1': 9, 'ASP:plan': 24, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 8, 'PHE:plan': 7, 'GLU:plan': 16, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 385 Time building chain proxies: 8.81, per 1000 atoms: 0.65 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: 3.53 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.44 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: 3.55 Time building geometry restraints manager: 4.20 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: 0.210 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: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.020 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.060 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.700 ------------------------------------------------------------------------------- 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 : 5.89 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP B 474 HIS 0.005 0.001 HIS C 131 PHE 0.024 0.001 PHE A 467 TYR 0.015 0.001 TYR B 465 ARG 0.002 0.000 ARG C 192 Details of bonding type rmsd hydrogen bonds : bond 0.26435 ( 173) hydrogen bonds : angle 9.41421 ( 426) covalent geometry : bond 0.00284 (14002) covalent geometry : angle 0.60567 (19252) *********************** 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 : 1.525 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: 0.6872 (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: 0.7677 (m100) REVERT: B 78 ARG cc_start: 0.5631 (mtt180) cc_final: 0.5389 (mtt180) REVERT: B 220 LYS cc_start: 0.8360 (mppt) cc_final: 0.8082 (mttt) REVERT: B 356 PHE cc_start: 0.7971 (m-80) cc_final: 0.7753 (m-80) REVERT: B 498 MET cc_start: 0.8148 (mtp) cc_final: 0.7395 (mtp) REVERT: B 530 TYR cc_start: 0.8624 (m-80) cc_final: 0.7574 (m-80) REVERT: C 60 PHE cc_start: 0.7466 (p90) cc_final: 0.7224 (p90) REVERT: C 182 TYR cc_start: 0.8385 (m-80) cc_final: 0.8055 (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: 0.5172 (mp0) outliers start: 2 outliers final: 2 residues processed: 326 average time/residue: 0.2678 time to fit residues: 123.7117 Evaluate side-chains 246 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 244 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 146 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 chunk 109 optimal weight: 0.9980 chunk 169 optimal weight: 0.0070 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 107 HIS A 282 HIS A 311 HIS A 445 HIS A 483 GLN B 102 HIS 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.179749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.165176 restraints weight = 17243.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.156273 restraints weight = 21243.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.155778 restraints weight = 20582.525| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1392 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 : 0.606 6.868 19252 Z= 0.305 Chirality : 0.047 0.169 2223 Planarity : 0.005 0.087 2509 Dihedral : 4.447 23.845 1985 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.37 % Favored : 88.57 % Rotamer: Outliers : 0.08 % Allowed : 4.18 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.90 (0.17), residues: 1873 helix: -1.15 (0.42), residues: 143 sheet: -3.43 (0.21), residues: 440 loop : -3.70 (0.15), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 474 HIS 0.007 0.001 HIS C 131 PHE 0.016 0.001 PHE A 467 TYR 0.019 0.001 TYR C 465 ARG 0.005 0.001 ARG C 192 Details of bonding type rmsd hydrogen bonds : bond 0.03559 ( 173) hydrogen bonds : angle 6.53640 ( 426) covalent geometry : bond 0.00244 (14002) covalent geometry : angle 0.60633 (19252) *********************** 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 284 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 283 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 TYR cc_start: 0.8795 (m-10) cc_final: 0.8545 (m-10) REVERT: A 315 ASN cc_start: 0.8116 (t0) cc_final: 0.7031 (p0) REVERT: A 386 PRO cc_start: 0.7671 (Cg_exo) cc_final: 0.7400 (Cg_endo) REVERT: A 416 ASN cc_start: 0.9158 (m-40) cc_final: 0.8945 (m-40) REVERT: A 461 TRP cc_start: 0.8240 (m-90) cc_final: 0.7679 (m100) REVERT: B 78 ARG cc_start: 0.5346 (mtt180) cc_final: 0.5029 (mtt180) REVERT: B 415 ASN cc_start: 0.8566 (p0) cc_final: 0.8154 (m110) REVERT: B 416 ASN cc_start: 0.9021 (m-40) cc_final: 0.8728 (m-40) REVERT: B 498 MET cc_start: 0.8131 (mtp) cc_final: 0.7372 (mtp) REVERT: B 530 TYR cc_start: 0.8586 (m-80) cc_final: 0.7428 (m-80) REVERT: B 614 TYR cc_start: 0.8202 (t80) cc_final: 0.7908 (t80) REVERT: C 27 ASN cc_start: 0.7722 (m110) cc_final: 0.7182 (m110) REVERT: C 182 TYR cc_start: 0.8314 (m-80) cc_final: 0.8069 (m-80) REVERT: C 440 LYS cc_start: 0.8478 (mmtt) cc_final: 0.8159 (mmmt) REVERT: C 505 GLU cc_start: 0.6879 (tm-30) cc_final: 0.5087 (mp0) outliers start: 1 outliers final: 0 residues processed: 284 average time/residue: 0.2388 time to fit residues: 100.6768 Evaluate side-chains 226 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 114 optimal weight: 0.0870 chunk 47 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 overall best weight: 3.8166 ------------------------------------------------------------------------------- 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 B 503 HIS B 565 HIS C 102 HIS C 107 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.170159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.161095 restraints weight = 18051.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.151034 restraints weight = 31872.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.148863 restraints weight = 27056.934| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 14002 Z= 0.248 Angle : 0.731 9.517 19252 Z= 0.376 Chirality : 0.051 0.173 2223 Planarity : 0.006 0.102 2509 Dihedral : 5.509 26.806 1985 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 17.57 % Favored : 82.38 % Rotamer: Outliers : 0.15 % Allowed : 6.66 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.86 (0.17), residues: 1873 helix: -1.16 (0.43), residues: 141 sheet: -3.02 (0.22), residues: 436 loop : -3.82 (0.15), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 474 HIS 0.010 0.002 HIS B 445 PHE 0.026 0.002 PHE A 60 TYR 0.028 0.003 TYR B 465 ARG 0.006 0.001 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.04364 ( 173) hydrogen bonds : angle 6.14371 ( 426) covalent geometry : bond 0.00568 (14002) covalent geometry : angle 0.73100 (19252) *********************** 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 283 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 281 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 TRP cc_start: 0.8432 (m-90) cc_final: 0.7788 (m100) REVERT: B 455 LEU cc_start: 0.8940 (tp) cc_final: 0.8622 (tp) REVERT: B 498 MET cc_start: 0.8249 (mtp) cc_final: 0.7385 (mtp) REVERT: B 530 TYR cc_start: 0.8591 (m-80) cc_final: 0.7871 (m-80) REVERT: C 27 ASN cc_start: 0.7770 (m110) cc_final: 0.7446 (m-40) REVERT: C 61 ASN cc_start: 0.8818 (t0) cc_final: 0.8450 (t0) REVERT: C 440 LYS cc_start: 0.8693 (mmtt) cc_final: 0.8470 (mmmt) REVERT: C 466 MET cc_start: 0.7813 (tpt) cc_final: 0.7588 (tpt) REVERT: C 505 GLU cc_start: 0.7334 (tm-30) cc_final: 0.5411 (mp0) outliers start: 2 outliers final: 0 residues processed: 282 average time/residue: 0.2172 time to fit residues: 93.6588 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 : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 25 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 69 optimal weight: 0.0010 chunk 119 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 33 optimal weight: 0.0270 chunk 174 optimal weight: 7.9990 chunk 166 optimal weight: 0.0470 chunk 41 optimal weight: 0.1980 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.1742 ------------------------------------------------------------------------------- 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 311 HIS ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 HIS A 569 ASN B 475 ASN C 96 GLN C 226 HIS C 445 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.179945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.170530 restraints weight = 17218.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.160124 restraints weight = 31388.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.157786 restraints weight = 26587.946| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14002 Z= 0.107 Angle : 0.612 7.445 19252 Z= 0.308 Chirality : 0.046 0.195 2223 Planarity : 0.006 0.095 2509 Dihedral : 4.724 24.254 1985 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.95 % Favored : 89.00 % Rotamer: Outliers : 0.08 % Allowed : 3.56 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (0.17), residues: 1873 helix: -0.67 (0.44), residues: 143 sheet: -2.90 (0.21), residues: 486 loop : -3.48 (0.16), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 474 HIS 0.004 0.001 HIS C 226 PHE 0.019 0.001 PHE A 101 TYR 0.018 0.001 TYR C 530 ARG 0.004 0.000 ARG A 163 Details of bonding type rmsd hydrogen bonds : bond 0.02679 ( 173) hydrogen bonds : angle 5.58332 ( 426) covalent geometry : bond 0.00243 (14002) covalent geometry : angle 0.61151 (19252) *********************** 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 : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 TYR cc_start: 0.8763 (m-10) cc_final: 0.8514 (m-10) REVERT: A 315 ASN cc_start: 0.7806 (t0) cc_final: 0.6506 (p0) REVERT: A 461 TRP cc_start: 0.8176 (m-90) cc_final: 0.7659 (m100) REVERT: A 530 TYR cc_start: 0.8435 (m-80) cc_final: 0.7665 (m-80) REVERT: B 313 SER cc_start: 0.9198 (p) cc_final: 0.8939 (m) REVERT: B 411 GLU cc_start: 0.8053 (mp0) cc_final: 0.7693 (mp0) REVERT: B 498 MET cc_start: 0.8085 (mtp) cc_final: 0.7303 (mtp) REVERT: B 530 TYR cc_start: 0.8504 (m-80) cc_final: 0.7594 (m-80) REVERT: C 27 ASN cc_start: 0.7740 (m110) cc_final: 0.7392 (m110) REVERT: C 182 TYR cc_start: 0.8348 (m-80) cc_final: 0.8077 (m-80) REVERT: C 440 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8322 (mmmt) REVERT: C 466 MET cc_start: 0.7752 (tpt) cc_final: 0.7447 (tpt) REVERT: C 505 GLU cc_start: 0.6912 (tm-30) cc_final: 0.5544 (mp0) outliers start: 1 outliers final: 0 residues processed: 291 average time/residue: 0.2332 time to fit residues: 102.6058 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 : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 64 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 112 optimal weight: 0.0070 chunk 75 optimal weight: 0.5980 chunk 93 optimal weight: 0.0040 chunk 43 optimal weight: 0.1980 chunk 29 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 chunk 163 optimal weight: 2.9990 overall best weight: 0.2810 ------------------------------------------------------------------------------- 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 B 23 GLN B 445 HIS C 96 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.182344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.173810 restraints weight = 17289.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.162808 restraints weight = 29911.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.160038 restraints weight = 29776.112| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2160 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= 0.096 Angle : 0.597 7.404 19252 Z= 0.300 Chirality : 0.046 0.183 2223 Planarity : 0.006 0.107 2509 Dihedral : 4.533 25.290 1985 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.37 % Favored : 88.57 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.18), residues: 1873 helix: -0.45 (0.45), residues: 143 sheet: -2.61 (0.22), residues: 478 loop : -3.32 (0.16), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 474 HIS 0.002 0.000 HIS B 102 PHE 0.019 0.001 PHE B 467 TYR 0.023 0.001 TYR A 178 ARG 0.006 0.001 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.02569 ( 173) hydrogen bonds : angle 5.38676 ( 426) covalent geometry : bond 0.00223 (14002) covalent geometry : angle 0.59686 (19252) *********************** 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 276 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 TRP cc_start: 0.8119 (m-90) cc_final: 0.7654 (m100) REVERT: B 221 MET cc_start: 0.7184 (tpp) cc_final: 0.6979 (tpp) REVERT: B 411 GLU cc_start: 0.8088 (mp0) cc_final: 0.7649 (mp0) REVERT: C 27 ASN cc_start: 0.7761 (m110) cc_final: 0.7357 (m110) REVERT: C 72 PHE cc_start: 0.8169 (p90) cc_final: 0.7742 (p90) REVERT: C 505 GLU cc_start: 0.6913 (tm-30) cc_final: 0.5428 (mp0) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.2284 time to fit residues: 96.1975 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 : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 114 optimal weight: 0.9980 chunk 138 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 20 optimal weight: 0.3980 chunk 74 optimal weight: 0.0770 chunk 162 optimal weight: 0.0670 chunk 67 optimal weight: 0.0980 chunk 165 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 overall best weight: 0.3076 ------------------------------------------------------------------------------- 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 445 HIS ** C 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.184075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.174540 restraints weight = 17292.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.161941 restraints weight = 24559.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.161069 restraints weight = 26058.346| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2379 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= 0.095 Angle : 0.577 7.513 19252 Z= 0.289 Chirality : 0.046 0.193 2223 Planarity : 0.006 0.101 2509 Dihedral : 4.302 23.677 1985 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.41 % Favored : 89.54 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.18), residues: 1873 helix: -0.31 (0.46), residues: 143 sheet: -2.49 (0.21), residues: 502 loop : -3.12 (0.16), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 474 HIS 0.003 0.000 HIS B 503 PHE 0.015 0.001 PHE C 60 TYR 0.017 0.001 TYR A 178 ARG 0.009 0.001 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.02315 ( 173) hydrogen bonds : angle 5.13882 ( 426) covalent geometry : bond 0.00220 (14002) covalent geometry : angle 0.57691 (19252) *********************** 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 279 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ARG cc_start: 0.6954 (ttt-90) cc_final: 0.5366 (ttm-80) REVERT: A 461 TRP cc_start: 0.8059 (m-90) cc_final: 0.7633 (m100) REVERT: B 411 GLU cc_start: 0.8002 (mp0) cc_final: 0.7678 (mp0) REVERT: B 456 MET cc_start: 0.5986 (tpt) cc_final: 0.5073 (tpt) REVERT: B 498 MET cc_start: 0.7596 (mtp) cc_final: 0.6960 (mtp) REVERT: B 503 HIS cc_start: 0.6874 (m90) cc_final: 0.6636 (m90) REVERT: B 530 TYR cc_start: 0.8311 (m-80) cc_final: 0.7565 (m-80) REVERT: C 27 ASN cc_start: 0.7759 (m110) cc_final: 0.7392 (m110) REVERT: C 72 PHE cc_start: 0.8100 (p90) cc_final: 0.7695 (p90) REVERT: C 182 TYR cc_start: 0.7850 (m-80) cc_final: 0.7589 (m-80) REVERT: C 505 GLU cc_start: 0.6748 (tm-30) cc_final: 0.5241 (mp0) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.2726 time to fit residues: 115.0299 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 : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 88 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 139 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 181 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 142 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 499 GLN B 445 HIS ** C 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.182903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.172842 restraints weight = 17234.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.172802 restraints weight = 25713.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.160000 restraints weight = 24626.908| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2408 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= 0.106 Angle : 0.596 7.558 19252 Z= 0.298 Chirality : 0.046 0.181 2223 Planarity : 0.006 0.113 2509 Dihedral : 4.366 23.863 1985 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.59 % Favored : 88.36 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.18), residues: 1873 helix: -0.32 (0.45), residues: 143 sheet: -2.46 (0.21), residues: 510 loop : -3.05 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 474 HIS 0.004 0.001 HIS B 80 PHE 0.024 0.001 PHE B 72 TYR 0.021 0.001 TYR A 178 ARG 0.008 0.001 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.02382 ( 173) hydrogen bonds : angle 5.05804 ( 426) covalent geometry : bond 0.00252 (14002) covalent geometry : angle 0.59616 (19252) *********************** 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 : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ARG cc_start: 0.7030 (ttt-90) cc_final: 0.5451 (ttm-80) REVERT: A 461 TRP cc_start: 0.8138 (m-90) cc_final: 0.7649 (m100) REVERT: B 411 GLU cc_start: 0.7952 (mp0) cc_final: 0.7588 (mp0) REVERT: B 498 MET cc_start: 0.7754 (mtp) cc_final: 0.7033 (mtp) REVERT: B 530 TYR cc_start: 0.8372 (m-80) cc_final: 0.7406 (m-80) REVERT: C 27 ASN cc_start: 0.7748 (m110) cc_final: 0.7335 (m110) REVERT: C 72 PHE cc_start: 0.8121 (p90) cc_final: 0.7714 (p90) REVERT: C 440 LYS cc_start: 0.8455 (mmtt) cc_final: 0.8051 (mmmt) REVERT: C 466 MET cc_start: 0.7606 (tpt) cc_final: 0.7313 (tpt) REVERT: C 505 GLU cc_start: 0.6906 (tm-30) cc_final: 0.5357 (mp0) REVERT: C 532 ILE cc_start: 0.8615 (mp) cc_final: 0.8357 (mt) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.3567 time to fit residues: 150.6470 Evaluate side-chains 213 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 2.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 71 optimal weight: 9.9990 chunk 149 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 176 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 45 optimal weight: 0.4980 chunk 90 optimal weight: 0.3980 chunk 62 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 overall best weight: 1.7582 ------------------------------------------------------------------------------- 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 499 GLN B 445 HIS ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN ** C 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.178232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.167901 restraints weight = 17485.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.155757 restraints weight = 26203.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.156045 restraints weight = 21975.145| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2398 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= 0.137 Angle : 0.630 7.738 19252 Z= 0.317 Chirality : 0.047 0.216 2223 Planarity : 0.006 0.114 2509 Dihedral : 4.640 25.224 1985 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.51 % Favored : 86.44 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.18), residues: 1873 helix: -0.48 (0.44), residues: 143 sheet: -2.45 (0.21), residues: 519 loop : -3.09 (0.17), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 474 HIS 0.008 0.001 HIS C 80 PHE 0.022 0.002 PHE B 72 TYR 0.028 0.002 TYR B 465 ARG 0.010 0.001 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.02597 ( 173) hydrogen bonds : angle 5.18245 ( 426) covalent geometry : bond 0.00313 (14002) covalent geometry : angle 0.62952 (19252) *********************** 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 267 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 2.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.7493 (tt) cc_final: 0.7292 (tt) REVERT: A 179 TYR cc_start: 0.8742 (m-10) cc_final: 0.8407 (m-10) REVERT: A 461 TRP cc_start: 0.8154 (m-90) cc_final: 0.7589 (m100) REVERT: B 455 LEU cc_start: 0.8815 (tp) cc_final: 0.8601 (tp) REVERT: B 498 MET cc_start: 0.8012 (mtp) cc_final: 0.7271 (mtp) REVERT: B 530 TYR cc_start: 0.8382 (m-80) cc_final: 0.7659 (m-80) REVERT: B 605 GLU cc_start: 0.7158 (pm20) cc_final: 0.6811 (tp30) REVERT: C 27 ASN cc_start: 0.7836 (m-40) cc_final: 0.7272 (m110) REVERT: C 72 PHE cc_start: 0.8195 (p90) cc_final: 0.7768 (p90) REVERT: C 199 SER cc_start: 0.8789 (t) cc_final: 0.8233 (p) REVERT: C 440 LYS cc_start: 0.8541 (mmtt) cc_final: 0.8254 (mmmt) REVERT: C 466 MET cc_start: 0.7803 (tpt) cc_final: 0.7481 (tpt) REVERT: C 505 GLU cc_start: 0.6951 (tm-30) cc_final: 0.5564 (mp0) REVERT: C 532 ILE cc_start: 0.8716 (mp) cc_final: 0.8503 (mt) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.2897 time to fit residues: 120.7729 Evaluate side-chains 210 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 3.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 89 optimal weight: 0.0970 chunk 153 optimal weight: 0.2980 chunk 142 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 102 optimal weight: 0.0010 chunk 16 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS A 499 GLN B 445 HIS ** C 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.181819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.172890 restraints weight = 17137.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.161318 restraints weight = 26353.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.159124 restraints weight = 26902.568| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2579 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= 0.098 Angle : 0.605 7.584 19252 Z= 0.302 Chirality : 0.046 0.243 2223 Planarity : 0.006 0.116 2509 Dihedral : 4.380 23.909 1985 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.68 % Favored : 89.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.18), residues: 1873 helix: -0.34 (0.45), residues: 143 sheet: -2.24 (0.22), residues: 502 loop : -2.91 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 474 HIS 0.007 0.001 HIS B 482 PHE 0.021 0.001 PHE B 72 TYR 0.020 0.001 TYR B 465 ARG 0.008 0.001 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.02260 ( 173) hydrogen bonds : angle 5.00344 ( 426) covalent geometry : bond 0.00230 (14002) covalent geometry : angle 0.60472 (19252) *********************** 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 267 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 ARG cc_start: 0.7038 (ttt-90) cc_final: 0.5818 (ttm-80) REVERT: A 179 TYR cc_start: 0.8670 (m-10) cc_final: 0.8411 (m-10) REVERT: A 368 VAL cc_start: 0.9276 (t) cc_final: 0.8983 (p) REVERT: A 386 PRO cc_start: 0.7539 (Cg_exo) cc_final: 0.7185 (Cg_endo) REVERT: A 461 TRP cc_start: 0.8103 (m-90) cc_final: 0.7644 (m100) REVERT: B 411 GLU cc_start: 0.7843 (mp0) cc_final: 0.7633 (mp0) REVERT: B 483 GLN cc_start: 0.9087 (tm-30) cc_final: 0.8879 (tm-30) REVERT: C 27 ASN cc_start: 0.7921 (m-40) cc_final: 0.7462 (m-40) REVERT: C 72 PHE cc_start: 0.8175 (p90) cc_final: 0.7752 (p90) REVERT: C 505 GLU cc_start: 0.6857 (tm-30) cc_final: 0.5639 (mp0) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.2201 time to fit residues: 89.1919 Evaluate side-chains 218 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 180 optimal weight: 10.0000 chunk 86 optimal weight: 0.0970 chunk 95 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 153 optimal weight: 0.2980 chunk 18 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 overall best weight: 1.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS A 475 ASN A 499 GLN B 445 HIS ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.179779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3861 r_free = 0.3861 target = 0.169604 restraints weight = 17530.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.155568 restraints weight = 27616.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.156241 restraints weight = 25144.198| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2569 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= 0.123 Angle : 0.623 8.092 19252 Z= 0.312 Chirality : 0.047 0.244 2223 Planarity : 0.006 0.117 2509 Dihedral : 4.497 23.813 1985 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.29 % Favored : 86.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.19), residues: 1873 helix: -0.36 (0.45), residues: 143 sheet: -2.30 (0.22), residues: 508 loop : -2.90 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 474 HIS 0.005 0.001 HIS C 80 PHE 0.022 0.001 PHE B 72 TYR 0.026 0.002 TYR B 465 ARG 0.010 0.001 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.02542 ( 173) hydrogen bonds : angle 5.10105 ( 426) covalent geometry : bond 0.00290 (14002) covalent geometry : angle 0.62266 (19252) ********************** 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 267 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8052 (tm-30) REVERT: A 163 ARG cc_start: 0.6931 (ttt-90) cc_final: 0.5685 (ttm-80) REVERT: A 179 TYR cc_start: 0.8624 (m-10) cc_final: 0.8301 (m-10) REVERT: A 386 PRO cc_start: 0.7613 (Cg_exo) cc_final: 0.7288 (Cg_endo) REVERT: A 461 TRP cc_start: 0.8138 (m-90) cc_final: 0.7629 (m100) REVERT: B 212 ARG cc_start: 0.7963 (tmm-80) cc_final: 0.7759 (ttp-170) REVERT: B 411 GLU cc_start: 0.8005 (mp0) cc_final: 0.7738 (mp0) REVERT: B 530 TYR cc_start: 0.8398 (m-80) cc_final: 0.8047 (m-80) REVERT: B 605 GLU cc_start: 0.7083 (pm20) cc_final: 0.6736 (tp30) REVERT: C 27 ASN cc_start: 0.7992 (m-40) cc_final: 0.7494 (m110) REVERT: C 72 PHE cc_start: 0.8178 (p90) cc_final: 0.7768 (p90) REVERT: C 199 SER cc_start: 0.8771 (t) cc_final: 0.8205 (p) REVERT: C 463 ILE cc_start: 0.9045 (tt) cc_final: 0.8676 (tt) REVERT: C 466 MET cc_start: 0.7723 (tpt) cc_final: 0.7371 (tpt) REVERT: C 505 GLU cc_start: 0.6906 (tm-30) cc_final: 0.5518 (mp0) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.2463 time to fit residues: 100.1402 Evaluate side-chains 216 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 70 optimal weight: 0.0170 chunk 183 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 chunk 142 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 499 GLN B 445 HIS ** C 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.182364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.173164 restraints weight = 17566.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.159474 restraints weight = 24036.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.159081 restraints weight = 21875.349| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2730 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= 0.098 Angle : 0.602 7.608 19252 Z= 0.301 Chirality : 0.046 0.232 2223 Planarity : 0.006 0.115 2509 Dihedral : 4.319 23.676 1985 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.16 % Favored : 88.79 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.19), residues: 1873 helix: -0.36 (0.45), residues: 143 sheet: -2.17 (0.23), residues: 491 loop : -2.83 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 474 HIS 0.005 0.000 HIS C 80 PHE 0.024 0.001 PHE A 564 TYR 0.021 0.001 TYR B 465 ARG 0.009 0.001 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.02299 ( 173) hydrogen bonds : angle 5.01938 ( 426) covalent geometry : bond 0.00233 (14002) covalent geometry : angle 0.60243 (19252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4593.76 seconds wall clock time: 83 minutes 58.01 seconds (5038.01 seconds total)