Starting phenix.real_space_refine on Thu Sep 26 14:48:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l2t_0814/09_2024/6l2t_0814.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l2t_0814/09_2024/6l2t_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l2t_0814/09_2024/6l2t_0814.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l2t_0814/09_2024/6l2t_0814.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l2t_0814/09_2024/6l2t_0814.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l2t_0814/09_2024/6l2t_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-5461/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: 7.82, per 1000 atoms: 0.57 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: 2.96 Conformation dependent library (CDL) restraints added in 1.7 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: 1.43 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: 3.33 Time building geometry restraints manager: 3.51 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.510 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.050 ------------------------------------------------------------------------------- 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= 0.190 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 *********************** 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 fitting. rotamer outliers: 2 poor density : 324 time to evaluate : 1.403 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: 0.2646 time to fit residues: 122.2476 Evaluate side-chains 246 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 244 time to evaluate : 1.430 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 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= 0.163 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 283 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 TYR cc_start: 0.8766 (m-10) cc_final: 0.8550 (m-10) REVERT: A 315 ASN cc_start: 0.8065 (t0) cc_final: 0.7012 (p0) REVERT: A 386 PRO cc_start: 0.7700 (Cg_exo) cc_final: 0.7428 (Cg_endo) REVERT: A 461 TRP cc_start: 0.8222 (m-90) cc_final: 0.7719 (m100) REVERT: B 78 ARG cc_start: 0.5382 (mtt180) cc_final: 0.5058 (mtt180) REVERT: B 411 GLU cc_start: 0.7876 (mp0) cc_final: 0.7647 (mp0) REVERT: B 415 ASN cc_start: 0.8563 (p0) cc_final: 0.8198 (m110) REVERT: B 416 ASN cc_start: 0.8979 (m-40) cc_final: 0.8698 (m-40) REVERT: B 498 MET cc_start: 0.8168 (mtp) cc_final: 0.7459 (mtp) REVERT: B 530 TYR cc_start: 0.8599 (m-80) cc_final: 0.7450 (m-80) REVERT: B 614 TYR cc_start: 0.8250 (t80) cc_final: 0.7914 (t80) REVERT: C 27 ASN cc_start: 0.7719 (m110) cc_final: 0.7237 (m110) REVERT: C 182 TYR cc_start: 0.8294 (m-80) cc_final: 0.8050 (m-80) REVERT: C 440 LYS cc_start: 0.8549 (mmtt) cc_final: 0.8200 (mmmt) REVERT: C 505 GLU cc_start: 0.6875 (tm-30) cc_final: 0.5197 (mp0) outliers start: 1 outliers final: 0 residues processed: 284 average time/residue: 0.2345 time to fit residues: 98.7582 Evaluate side-chains 226 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 170 optimal weight: 0.9980 chunk 183 optimal weight: 8.9990 chunk 151 optimal weight: 0.6980 chunk 168 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 136 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 311 HIS A 445 HIS B 503 HIS B 565 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14002 Z= 0.176 Angle : 0.600 7.267 19252 Z= 0.300 Chirality : 0.046 0.166 2223 Planarity : 0.005 0.097 2509 Dihedral : 4.463 24.195 1985 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.69 % Favored : 88.25 % Rotamer: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.52 (0.17), residues: 1873 helix: -0.86 (0.43), residues: 143 sheet: -2.91 (0.21), residues: 474 loop : -3.53 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 474 HIS 0.003 0.001 HIS C 108 PHE 0.026 0.001 PHE A 60 TYR 0.025 0.001 TYR B 413 ARG 0.006 0.001 ARG A 308 *********************** 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 280 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 TYR cc_start: 0.8757 (m-10) cc_final: 0.8543 (m-10) REVERT: A 315 ASN cc_start: 0.8044 (t0) cc_final: 0.6913 (p0) REVERT: A 386 PRO cc_start: 0.7738 (Cg_exo) cc_final: 0.7495 (Cg_endo) REVERT: A 461 TRP cc_start: 0.8178 (m-90) cc_final: 0.7712 (m100) REVERT: B 78 ARG cc_start: 0.5441 (mtt180) cc_final: 0.5095 (mtt180) REVERT: B 415 ASN cc_start: 0.8689 (p0) cc_final: 0.8174 (m110) REVERT: B 416 ASN cc_start: 0.9031 (m-40) cc_final: 0.8707 (m-40) REVERT: B 498 MET cc_start: 0.8224 (mtp) cc_final: 0.7400 (mtp) REVERT: B 530 TYR cc_start: 0.8445 (m-80) cc_final: 0.7435 (m-80) REVERT: C 27 ASN cc_start: 0.7940 (m110) cc_final: 0.7422 (m110) REVERT: C 182 TYR cc_start: 0.8329 (m-80) cc_final: 0.8045 (m-80) REVERT: C 440 LYS cc_start: 0.8678 (mmtt) cc_final: 0.8317 (mmmt) REVERT: C 456 MET cc_start: 0.7047 (tpt) cc_final: 0.6764 (tpp) REVERT: C 505 GLU cc_start: 0.6918 (tm-30) cc_final: 0.5231 (mp0) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.2460 time to fit residues: 104.4032 Evaluate side-chains 223 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS C 107 HIS C 416 ASN C 445 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14002 Z= 0.367 Angle : 0.728 9.281 19252 Z= 0.373 Chirality : 0.051 0.180 2223 Planarity : 0.006 0.096 2509 Dihedral : 5.499 26.521 1985 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 17.67 % Favored : 82.27 % Rotamer: Outliers : 0.08 % Allowed : 6.58 % Favored : 93.34 % 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: -4.69 (0.17), residues: 1873 helix: -1.10 (0.43), residues: 141 sheet: -2.92 (0.21), residues: 467 loop : -3.69 (0.15), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 474 HIS 0.010 0.002 HIS B 445 PHE 0.025 0.002 PHE B 564 TYR 0.036 0.003 TYR B 188 ARG 0.005 0.001 ARG A 163 *********************** 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 283 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 282 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 TRP cc_start: 0.8409 (m-90) cc_final: 0.7824 (m100) REVERT: B 80 HIS cc_start: 0.7118 (OUTLIER) cc_final: 0.5536 (t70) REVERT: B 455 LEU cc_start: 0.8869 (tp) cc_final: 0.8547 (tp) REVERT: C 27 ASN cc_start: 0.7741 (m110) cc_final: 0.7393 (m110) REVERT: C 182 TYR cc_start: 0.8433 (m-80) cc_final: 0.8121 (m-80) REVERT: C 199 SER cc_start: 0.8829 (t) cc_final: 0.8389 (p) REVERT: C 358 THR cc_start: 0.8888 (m) cc_final: 0.8641 (p) REVERT: C 440 LYS cc_start: 0.8662 (mmtt) cc_final: 0.8361 (mmmt) REVERT: C 505 GLU cc_start: 0.7099 (tm-30) cc_final: 0.5276 (mp0) outliers start: 1 outliers final: 0 residues processed: 283 average time/residue: 0.2166 time to fit residues: 94.0427 Evaluate side-chains 230 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 229 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 154 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN B 445 HIS B 503 HIS C 96 GLN C 226 HIS C 445 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14002 Z= 0.268 Angle : 0.667 9.080 19252 Z= 0.340 Chirality : 0.049 0.208 2223 Planarity : 0.006 0.108 2509 Dihedral : 5.278 26.848 1985 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 14.04 % Favored : 85.90 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % 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: -4.57 (0.17), residues: 1873 helix: -0.89 (0.43), residues: 141 sheet: -2.91 (0.21), residues: 495 loop : -3.57 (0.16), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 474 HIS 0.006 0.001 HIS C 226 PHE 0.022 0.002 PHE A 137 TYR 0.018 0.002 TYR B 465 ARG 0.004 0.000 ARG A 192 *********************** 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 279 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 TRP cc_start: 0.8348 (m-90) cc_final: 0.7840 (m100) REVERT: B 498 MET cc_start: 0.8190 (mtp) cc_final: 0.7266 (mtp) REVERT: B 530 TYR cc_start: 0.8527 (m-80) cc_final: 0.7787 (m-80) REVERT: C 27 ASN cc_start: 0.7763 (m110) cc_final: 0.7457 (m-40) REVERT: C 61 ASN cc_start: 0.8958 (t0) cc_final: 0.8750 (t0) REVERT: C 199 SER cc_start: 0.8828 (t) cc_final: 0.8343 (p) REVERT: C 440 LYS cc_start: 0.8840 (mmtt) cc_final: 0.8589 (mmmt) REVERT: C 505 GLU cc_start: 0.7006 (tm-30) cc_final: 0.5533 (mp0) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.2427 time to fit residues: 102.2636 Evaluate side-chains 224 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 8.9990 chunk 162 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 180 optimal weight: 3.9990 chunk 150 optimal weight: 0.4980 chunk 83 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 59 optimal weight: 0.5980 chunk 94 optimal weight: 0.0030 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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 131 HIS A 311 HIS ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 ASN B 445 HIS ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 HIS B 548 ASN C 445 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2235 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= 0.158 Angle : 0.617 7.634 19252 Z= 0.311 Chirality : 0.047 0.200 2223 Planarity : 0.006 0.106 2509 Dihedral : 4.756 24.252 1985 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.91 % Favored : 88.04 % Rotamer: Outliers : 0.08 % Allowed : 2.86 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.17 (0.18), residues: 1873 helix: -0.60 (0.45), residues: 140 sheet: -2.73 (0.23), residues: 430 loop : -3.27 (0.16), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 336 HIS 0.009 0.001 HIS A 131 PHE 0.017 0.001 PHE C 60 TYR 0.024 0.001 TYR B 614 ARG 0.007 0.001 ARG A 192 *********************** 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 273 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 272 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLN cc_start: 0.8409 (tp40) cc_final: 0.8068 (tp40) REVERT: A 386 PRO cc_start: 0.7496 (Cg_exo) cc_final: 0.7185 (Cg_endo) REVERT: A 461 TRP cc_start: 0.8238 (m-90) cc_final: 0.7812 (m100) REVERT: B 411 GLU cc_start: 0.8002 (mp0) cc_final: 0.7627 (mp0) REVERT: B 456 MET cc_start: 0.6132 (tpt) cc_final: 0.5930 (tpt) REVERT: B 498 MET cc_start: 0.8056 (mtp) cc_final: 0.7176 (mtp) REVERT: B 530 TYR cc_start: 0.8344 (m-80) cc_final: 0.7724 (m-80) REVERT: C 27 ASN cc_start: 0.7754 (m110) cc_final: 0.7310 (m110) REVERT: C 61 ASN cc_start: 0.8954 (t0) cc_final: 0.8542 (t0) REVERT: C 440 LYS cc_start: 0.8751 (mmtt) cc_final: 0.8485 (mmmt) REVERT: C 505 GLU cc_start: 0.6939 (tm-30) cc_final: 0.5750 (mp0) outliers start: 1 outliers final: 0 residues processed: 273 average time/residue: 0.2318 time to fit residues: 93.9434 Evaluate side-chains 225 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 102 optimal weight: 0.0370 chunk 152 optimal weight: 0.0370 chunk 101 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 109 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 overall best weight: 0.3936 ------------------------------------------------------------------------------- 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 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 445 HIS B 548 ASN ** C 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 445 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2338 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= 0.157 Angle : 0.608 7.499 19252 Z= 0.304 Chirality : 0.046 0.162 2223 Planarity : 0.006 0.113 2509 Dihedral : 4.566 24.846 1985 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.69 % Favored : 88.25 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % 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: -3.93 (0.18), residues: 1873 helix: -0.37 (0.45), residues: 143 sheet: -2.51 (0.23), residues: 423 loop : -3.13 (0.16), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 474 HIS 0.004 0.000 HIS C 80 PHE 0.019 0.001 PHE C 467 TYR 0.019 0.001 TYR B 614 ARG 0.006 0.001 ARG A 192 *********************** 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 270 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 GLN cc_start: 0.8405 (tp40) cc_final: 0.8029 (tp40) REVERT: A 386 PRO cc_start: 0.7597 (Cg_exo) cc_final: 0.7298 (Cg_endo) REVERT: A 461 TRP cc_start: 0.8158 (m-90) cc_final: 0.7796 (m100) REVERT: A 530 TYR cc_start: 0.8259 (m-80) cc_final: 0.7597 (m-80) REVERT: B 411 GLU cc_start: 0.7948 (mp0) cc_final: 0.7544 (mp0) REVERT: B 456 MET cc_start: 0.6157 (tpt) cc_final: 0.5892 (tpt) REVERT: C 61 ASN cc_start: 0.8911 (t0) cc_final: 0.8510 (t0) REVERT: C 505 GLU cc_start: 0.6740 (tm-30) cc_final: 0.5575 (mp0) REVERT: C 532 ILE cc_start: 0.8530 (mp) cc_final: 0.8230 (mt) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2281 time to fit residues: 91.9938 Evaluate side-chains 214 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 GLN B 23 GLN B 445 HIS B 548 ASN ** C 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 445 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14002 Z= 0.294 Angle : 0.689 8.026 19252 Z= 0.350 Chirality : 0.049 0.235 2223 Planarity : 0.006 0.119 2509 Dihedral : 5.163 26.575 1985 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 15.48 % Favored : 84.46 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: -4.17 (0.18), residues: 1873 helix: -0.66 (0.45), residues: 140 sheet: -2.61 (0.21), residues: 488 loop : -3.30 (0.16), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 474 HIS 0.009 0.001 HIS B 80 PHE 0.023 0.002 PHE A 584 TYR 0.026 0.002 TYR B 465 ARG 0.007 0.001 ARG A 192 *********************** 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 271 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 1.541 Fit side-chains REVERT: A 53 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8206 (tm-30) REVERT: A 179 TYR cc_start: 0.8708 (m-10) cc_final: 0.8256 (m-10) REVERT: A 386 PRO cc_start: 0.7817 (Cg_exo) cc_final: 0.7535 (Cg_endo) REVERT: A 461 TRP cc_start: 0.8359 (m-90) cc_final: 0.7809 (m100) REVERT: B 455 LEU cc_start: 0.8782 (tp) cc_final: 0.8517 (tp) REVERT: B 498 MET cc_start: 0.8296 (mtp) cc_final: 0.8047 (mtp) REVERT: B 530 TYR cc_start: 0.8470 (m-80) cc_final: 0.8145 (m-80) REVERT: B 605 GLU cc_start: 0.7564 (pm20) cc_final: 0.7055 (tp30) REVERT: C 27 ASN cc_start: 0.7754 (m110) cc_final: 0.7492 (m110) REVERT: C 61 ASN cc_start: 0.8972 (t0) cc_final: 0.8763 (t0) REVERT: C 221 MET cc_start: 0.7800 (mtt) cc_final: 0.7593 (mtp) REVERT: C 505 GLU cc_start: 0.7050 (tm-30) cc_final: 0.5591 (mp0) REVERT: C 532 ILE cc_start: 0.8728 (mp) cc_final: 0.8486 (mt) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.2275 time to fit residues: 93.0309 Evaluate side-chains 216 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 101 optimal weight: 0.0170 chunk 73 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 158 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 overall best weight: 2.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 GLN B 23 GLN B 445 HIS C 96 GLN ** C 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 445 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14002 Z= 0.233 Angle : 0.659 7.954 19252 Z= 0.335 Chirality : 0.048 0.205 2223 Planarity : 0.006 0.123 2509 Dihedral : 5.073 26.011 1985 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.24 % Favored : 86.71 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % 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: -4.10 (0.18), residues: 1873 helix: -0.64 (0.46), residues: 140 sheet: -2.62 (0.22), residues: 482 loop : -3.22 (0.16), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 474 HIS 0.006 0.001 HIS B 482 PHE 0.018 0.002 PHE A 467 TYR 0.030 0.002 TYR B 614 ARG 0.007 0.001 ARG A 192 *********************** 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 271 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 1.503 Fit side-chains REVERT: A 179 TYR cc_start: 0.8678 (m-10) cc_final: 0.8289 (m-10) REVERT: A 386 PRO cc_start: 0.7734 (Cg_exo) cc_final: 0.7452 (Cg_endo) REVERT: A 461 TRP cc_start: 0.8318 (m-90) cc_final: 0.7833 (m100) REVERT: B 411 GLU cc_start: 0.7904 (mp0) cc_final: 0.7598 (mp0) REVERT: B 530 TYR cc_start: 0.8427 (m-80) cc_final: 0.8194 (m-80) REVERT: C 61 ASN cc_start: 0.8982 (t0) cc_final: 0.8756 (t0) REVERT: C 466 MET cc_start: 0.7976 (tpp) cc_final: 0.7718 (tpp) REVERT: C 505 GLU cc_start: 0.7035 (tm-30) cc_final: 0.5740 (mp0) REVERT: C 530 TYR cc_start: 0.8464 (m-80) cc_final: 0.8178 (m-80) REVERT: C 532 ILE cc_start: 0.8694 (mp) cc_final: 0.8454 (mt) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.2249 time to fit residues: 91.5492 Evaluate side-chains 206 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS A 445 HIS ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 GLN B 23 GLN B 244 ASN B 445 HIS ** C 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 HIS C 445 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14002 Z= 0.229 Angle : 0.660 7.949 19252 Z= 0.335 Chirality : 0.048 0.207 2223 Planarity : 0.006 0.125 2509 Dihedral : 5.049 26.324 1985 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 15.11 % Favored : 84.84 % 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: -4.06 (0.18), residues: 1873 helix: -0.71 (0.45), residues: 140 sheet: -2.58 (0.23), residues: 460 loop : -3.19 (0.16), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 474 HIS 0.006 0.001 HIS B 80 PHE 0.018 0.002 PHE A 467 TYR 0.025 0.002 TYR B 614 ARG 0.007 0.001 ARG A 192 ********************** 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 270 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.553 Fit side-chains REVERT: A 53 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8243 (tm-30) REVERT: A 163 ARG cc_start: 0.7609 (ptm-80) cc_final: 0.6802 (ttm-80) REVERT: A 179 TYR cc_start: 0.8662 (m-10) cc_final: 0.8378 (m-10) REVERT: A 386 PRO cc_start: 0.7764 (Cg_exo) cc_final: 0.7482 (Cg_endo) REVERT: A 461 TRP cc_start: 0.8372 (m-90) cc_final: 0.7874 (m100) REVERT: B 411 GLU cc_start: 0.7976 (mp0) cc_final: 0.7624 (mp0) REVERT: B 455 LEU cc_start: 0.8741 (tp) cc_final: 0.8537 (tp) REVERT: B 530 TYR cc_start: 0.8421 (m-80) cc_final: 0.8070 (m-80) REVERT: B 605 GLU cc_start: 0.7306 (pm20) cc_final: 0.6924 (tp30) REVERT: C 61 ASN cc_start: 0.8924 (t0) cc_final: 0.8455 (t0) REVERT: C 466 MET cc_start: 0.7915 (tpp) cc_final: 0.7649 (tpp) REVERT: C 505 GLU cc_start: 0.7020 (tm-30) cc_final: 0.5743 (mp0) REVERT: C 530 TYR cc_start: 0.8348 (m-80) cc_final: 0.8028 (m-80) REVERT: C 532 ILE cc_start: 0.8692 (mp) cc_final: 0.8477 (mt) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2237 time to fit residues: 90.6821 Evaluate side-chains 223 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 136 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 0.0010 chunk 148 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS A 445 HIS ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 GLN B 244 ASN B 445 HIS B 503 HIS C 96 GLN ** C 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.176349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.166490 restraints weight = 17689.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.153719 restraints weight = 26854.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.153983 restraints weight = 22438.830| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14002 Z= 0.192 Angle : 0.645 7.837 19252 Z= 0.325 Chirality : 0.047 0.269 2223 Planarity : 0.006 0.124 2509 Dihedral : 4.904 25.607 1985 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.60 % Favored : 87.35 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -3.91 (0.18), residues: 1873 helix: -0.52 (0.45), residues: 142 sheet: -2.46 (0.23), residues: 466 loop : -3.11 (0.16), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 474 HIS 0.004 0.001 HIS B 80 PHE 0.018 0.001 PHE C 60 TYR 0.020 0.002 TYR B 465 ARG 0.008 0.001 ARG A 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2794.03 seconds wall clock time: 50 minutes 39.01 seconds (3039.01 seconds total)