Starting phenix.real_space_refine on Wed Jul 30 00:47:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ejl_48104/07_2025/9ejl_48104_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ejl_48104/07_2025/9ejl_48104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ejl_48104/07_2025/9ejl_48104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ejl_48104/07_2025/9ejl_48104.map" model { file = "/net/cci-nas-00/data/ceres_data/9ejl_48104/07_2025/9ejl_48104_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ejl_48104/07_2025/9ejl_48104_neut.cif" } resolution = 3.48 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= -0.000 sd= 0.009 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 51 5.16 5 C 7548 2.51 5 N 2061 2.21 5 O 2102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11764 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 6621 Classifications: {'peptide': 867} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 5, 'PTRANS': 52, 'TRANS': 809} Chain breaks: 3 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 8, 'GLU:plan': 20, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 183 Chain: "B" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3800 Classifications: {'peptide': 506} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 24, 'TRANS': 481} Chain breaks: 1 Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 414 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'TPO:plan-1': 2, 'ASP:plan': 18, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 233 Chain: "C" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1343 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 178} Chain breaks: 4 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 84 Time building chain proxies: 10.09, per 1000 atoms: 0.86 Number of scatterers: 11764 At special positions: 0 Unit cell: (96.1015, 122.21, 118.877, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 P 2 15.00 O 2102 8.00 N 2061 7.00 C 7548 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: 2.83 Conformation dependent library (CDL) restraints added in 1.8 seconds 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2912 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 26 sheets defined 18.9% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 13 through 20 removed outlier: 3.805A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.848A pdb=" N THR A 130 " --> pdb=" O PRO A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 removed outlier: 3.889A pdb=" N ARG A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 397 through 410 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 751 through 755 removed outlier: 3.619A pdb=" N ARG A 755 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 798 removed outlier: 3.684A pdb=" N HIS A 797 " --> pdb=" O LEU A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 840 Processing helix chain 'A' and resid 895 through 900 Processing helix chain 'B' and resid 46 through 58 Processing helix chain 'B' and resid 82 through 96 Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.810A pdb=" N TYR B 125 " --> pdb=" O ASP B 121 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 121 through 126' Processing helix chain 'B' and resid 181 through 186 removed outlier: 5.120A pdb=" N LYS B 184 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL B 186 " --> pdb=" O HIS B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 296 through 310 removed outlier: 3.601A pdb=" N GLN B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 348 removed outlier: 3.823A pdb=" N HIS B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 372 Processing helix chain 'B' and resid 416 through 420 Processing helix chain 'B' and resid 421 through 427 removed outlier: 3.661A pdb=" N LEU B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 449 removed outlier: 4.071A pdb=" N TRP B 436 " --> pdb=" O PHE B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 476 removed outlier: 3.849A pdb=" N LEU B 470 " --> pdb=" O THR B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 497 Processing helix chain 'B' and resid 511 through 518 Processing helix chain 'B' and resid 526 through 532 Processing helix chain 'B' and resid 548 through 552 Processing helix chain 'B' and resid 553 through 558 Processing helix chain 'B' and resid 567 through 572 Processing helix chain 'B' and resid 573 through 574 No H-bonds generated for 'chain 'B' and resid 573 through 574' Processing helix chain 'B' and resid 575 through 579 removed outlier: 3.797A pdb=" N GLU B 578 " --> pdb=" O ASP B 575 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE B 579 " --> pdb=" O GLN B 576 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 575 through 579' Processing helix chain 'C' and resid 39 through 51 Processing helix chain 'C' and resid 74 through 85 removed outlier: 3.715A pdb=" N TYR C 78 " --> pdb=" O ASN C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 207 Processing helix chain 'C' and resid 227 through 238 Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 25 removed outlier: 3.740A pdb=" N LEU A 923 " --> pdb=" O GLN A 22 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASN A 24 " --> pdb=" O PHE A 921 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N PHE A 921 " --> pdb=" O ASN A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 41 removed outlier: 6.535A pdb=" N GLY A 50 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU A 38 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA A 48 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TYR A 40 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE A 46 " --> pdb=" O TYR A 40 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA A 55 " --> pdb=" O THR A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 81 removed outlier: 3.517A pdb=" N GLN A 78 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU A 97 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N SER A 116 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU A 99 " --> pdb=" O ASP A 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 137 removed outlier: 4.234A pdb=" N VAL A 134 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N VAL A 155 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG A 167 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 10.989A pdb=" N GLN A 157 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 10.993A pdb=" N GLU A 165 " --> pdb=" O GLN A 157 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 191 through 197 removed outlier: 6.515A pdb=" N GLY A 207 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU A 194 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 205 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N GLU A 196 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N GLN A 203 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR A 225 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ASP A 217 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL A 223 " --> pdb=" O ASP A 217 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 233 through 238 removed outlier: 7.034A pdb=" N CYS A 248 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE A 236 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL A 246 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N TRP A 238 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU A 244 " --> pdb=" O TRP A 238 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG A 270 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 285 through 289 removed outlier: 4.156A pdb=" N ARG A 285 " --> pdb=" O GLN A 301 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N HIS A 313 " --> pdb=" O PHE A 328 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 334 through 338 removed outlier: 3.613A pdb=" N GLY A 334 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA A 352 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 387 through 394 removed outlier: 3.755A pdb=" N CYS A 389 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A 446 " --> pdb=" O HIS A 442 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR A 461 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ASP A 451 " --> pdb=" O LEU A 459 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 459 " --> pdb=" O ASP A 451 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 426 through 427 removed outlier: 3.742A pdb=" N THR A 426 " --> pdb=" O LEU A 934 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 934 " --> pdb=" O THR A 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 499 through 500 Processing sheet with id=AB3, first strand: chain 'A' and resid 507 through 512 removed outlier: 5.069A pdb=" N GLN A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL A 528 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU A 582 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL A 530 " --> pdb=" O PHE A 580 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLU A 543 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N GLN A 584 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL A 545 " --> pdb=" O GLN A 584 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLN A 586 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA A 547 " --> pdb=" O GLN A 586 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 538 through 540 Processing sheet with id=AB5, first strand: chain 'A' and resid 593 through 597 removed outlier: 3.500A pdb=" N SER A 593 " --> pdb=" O GLY A 606 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 623 " --> pdb=" O LEU A 613 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASP A 615 " --> pdb=" O GLN A 621 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLN A 621 " --> pdb=" O ASP A 615 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 651 through 652 Processing sheet with id=AB7, first strand: chain 'A' and resid 698 through 699 removed outlier: 6.630A pdb=" N TYR C 172 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 10.670A pdb=" N GLU C 217 " --> pdb=" O PRO C 190 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE C 192 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR C 245 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL C 218 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE C 243 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 698 through 699 removed outlier: 6.630A pdb=" N TYR C 172 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 10.670A pdb=" N GLU C 217 " --> pdb=" O PRO C 190 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE C 192 " --> pdb=" O VAL C 215 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 713 through 721 removed outlier: 6.384A pdb=" N GLY A 736 " --> pdb=" O ARG A 714 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU A 716 " --> pdb=" O TRP A 734 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TRP A 734 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N PHE A 718 " --> pdb=" O SER A 732 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N SER A 732 " --> pdb=" O PHE A 718 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASP A 720 " --> pdb=" O CYS A 730 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N CYS A 730 " --> pdb=" O ASP A 720 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR A 741 " --> pdb=" O THR A 737 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N SER A 746 " --> pdb=" O GLN A 764 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLN A 764 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG A 748 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA A 762 " --> pdb=" O ARG A 748 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE C 296 " --> pdb=" O GLN A 769 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 776 through 781 removed outlier: 6.101A pdb=" N THR A 823 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA A 829 " --> pdb=" O THR A 823 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 843 through 852 removed outlier: 6.869A pdb=" N LEU A 867 " --> pdb=" O ARG A 844 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL A 846 " --> pdb=" O ALA A 865 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA A 865 " --> pdb=" O VAL A 846 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL A 848 " --> pdb=" O HIS A 863 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N HIS A 863 " --> pdb=" O VAL A 848 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N HIS A 850 " --> pdb=" O GLU A 861 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU A 861 " --> pdb=" O HIS A 850 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASP A 872 " --> pdb=" O THR A 868 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE A 873 " --> pdb=" O ARG A 886 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARG A 886 " --> pdb=" O ILE A 873 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL A 875 " --> pdb=" O GLN A 884 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 912 through 914 removed outlier: 3.931A pdb=" N SER A 914 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 35 through 41 removed outlier: 3.590A pdb=" N VAL B 28 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ARG B 27 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE B 103 " --> pdb=" O ARG B 27 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LYS B 29 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL B 105 " --> pdb=" O LYS B 29 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR B 31 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LEU B 102 " --> pdb=" O ILE B 71 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 136 through 138 Processing sheet with id=AC6, first strand: chain 'B' and resid 254 through 262 removed outlier: 5.548A pdb=" N LEU B 256 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ARG B 272 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL B 268 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ARG B 262 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 320 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU B 333 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU B 318 " --> pdb=" O GLU B 333 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 384 through 386 removed outlier: 3.717A pdb=" N LEU B 385 " --> pdb=" O LYS B 393 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 26 through 32 removed outlier: 3.575A pdb=" N ARG C 28 " --> pdb=" O SER C 21 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLU C 18 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ILE C 91 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS C 20 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ILE C 93 " --> pdb=" O LYS C 20 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LYS C 22 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N LYS C 95 " --> pdb=" O LYS C 22 " (cutoff:3.500A) 403 hydrogen bonds defined for protein. 1080 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: 4.77 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3877 1.34 - 1.46: 2371 1.46 - 1.57: 5731 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 12055 Sorted by residual: bond pdb=" CG1 ILE A 56 " pdb=" CD1 ILE A 56 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.04e+00 bond pdb=" CG1 ILE A 79 " pdb=" CD1 ILE A 79 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.76e+00 bond pdb=" CA LYS C 167 " pdb=" C LYS C 167 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.10e-02 2.27e+03 7.09e-01 bond pdb=" CA VAL A 455 " pdb=" C VAL A 455 " ideal model delta sigma weight residual 1.518 1.528 -0.009 1.13e-02 7.83e+03 6.64e-01 bond pdb=" CG PRO A 587 " pdb=" CD PRO A 587 " ideal model delta sigma weight residual 1.512 1.492 0.020 2.70e-02 1.37e+03 5.70e-01 ... (remaining 12050 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 16093 1.67 - 3.34: 300 3.34 - 5.01: 31 5.01 - 6.67: 1 6.67 - 8.34: 4 Bond angle restraints: 16429 Sorted by residual: angle pdb=" N VAL A 455 " pdb=" CA VAL A 455 " pdb=" C VAL A 455 " ideal model delta sigma weight residual 112.98 109.48 3.50 1.25e+00 6.40e-01 7.86e+00 angle pdb=" C GLN B 308 " pdb=" N ALA B 309 " pdb=" CA ALA B 309 " ideal model delta sigma weight residual 120.31 124.18 -3.87 1.52e+00 4.33e-01 6.49e+00 angle pdb=" C GLN B 347 " pdb=" N ARG B 348 " pdb=" CA ARG B 348 " ideal model delta sigma weight residual 121.54 126.40 -4.86 1.91e+00 2.74e-01 6.46e+00 angle pdb=" CA LEU C 89 " pdb=" CB LEU C 89 " pdb=" CG LEU C 89 " ideal model delta sigma weight residual 116.30 124.64 -8.34 3.50e+00 8.16e-02 5.68e+00 angle pdb=" CA LEU C 59 " pdb=" CB LEU C 59 " pdb=" CG LEU C 59 " ideal model delta sigma weight residual 116.30 124.44 -8.14 3.50e+00 8.16e-02 5.41e+00 ... (remaining 16424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 6341 17.84 - 35.68: 584 35.68 - 53.52: 157 53.52 - 71.36: 34 71.36 - 89.20: 14 Dihedral angle restraints: 7130 sinusoidal: 2624 harmonic: 4506 Sorted by residual: dihedral pdb=" CA CYS A 384 " pdb=" C CYS A 384 " pdb=" N SER A 385 " pdb=" CA SER A 385 " ideal model delta harmonic sigma weight residual 180.00 161.81 18.19 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA GLN B 532 " pdb=" C GLN B 532 " pdb=" N LYS B 533 " pdb=" CA LYS B 533 " ideal model delta harmonic sigma weight residual 180.00 162.53 17.47 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ARG B 131 " pdb=" C ARG B 131 " pdb=" N TRP B 132 " pdb=" CA TRP B 132 " ideal model delta harmonic sigma weight residual -180.00 -163.40 -16.60 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 7127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1125 0.032 - 0.063: 470 0.063 - 0.095: 150 0.095 - 0.126: 108 0.126 - 0.158: 12 Chirality restraints: 1865 Sorted by residual: chirality pdb=" CA VAL A 624 " pdb=" N VAL A 624 " pdb=" C VAL A 624 " pdb=" CB VAL A 624 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.21e-01 chirality pdb=" CA VAL A 273 " pdb=" N VAL A 273 " pdb=" C VAL A 273 " pdb=" CB VAL A 273 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CA VAL C 246 " pdb=" N VAL C 246 " pdb=" C VAL C 246 " pdb=" CB VAL C 246 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.74e-01 ... (remaining 1862 not shown) Planarity restraints: 2127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 854 " 0.245 9.50e-02 1.11e+02 1.11e-01 9.50e+00 pdb=" NE ARG A 854 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 854 " 0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG A 854 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 854 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 132 " -0.013 2.00e-02 2.50e+03 1.40e-02 4.87e+00 pdb=" CG TRP B 132 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP B 132 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 132 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 132 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 132 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 132 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 132 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 132 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 132 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 845 " 0.156 9.50e-02 1.11e+02 7.07e-02 3.96e+00 pdb=" NE ARG A 845 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 845 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A 845 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 845 " 0.000 2.00e-02 2.50e+03 ... (remaining 2124 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 543 2.73 - 3.27: 10672 3.27 - 3.81: 17789 3.81 - 4.36: 21090 4.36 - 4.90: 38099 Nonbonded interactions: 88193 Sorted by model distance: nonbonded pdb=" O GLY C 201 " pdb=" OG SER C 205 " model vdw 2.181 3.040 nonbonded pdb=" O ALA C 203 " pdb=" OG1 THR C 206 " model vdw 2.261 3.040 nonbonded pdb=" OH TYR B 376 " pdb=" O THR B 395 " model vdw 2.262 3.040 nonbonded pdb=" OE2 GLU B 120 " pdb=" OH TYR B 125 " model vdw 2.265 3.040 nonbonded pdb=" O GLY B 457 " pdb=" OG SER B 458 " model vdw 2.270 3.040 ... (remaining 88188 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.720 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: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 34.280 Find NCS groups from input model: 0.150 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: 0.020 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 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 0.056 12055 Z= 0.118 Angle : 0.560 8.343 16429 Z= 0.297 Chirality : 0.045 0.158 1865 Planarity : 0.005 0.111 2127 Dihedral : 15.648 89.204 4218 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.60 % Allowed : 18.45 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % 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: -0.70 (0.22), residues: 1536 helix: 0.67 (0.34), residues: 221 sheet: 0.20 (0.25), residues: 456 loop : -1.16 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 132 HIS 0.005 0.001 HIS A 561 PHE 0.019 0.001 PHE B 148 TYR 0.016 0.001 TYR A 254 ARG 0.025 0.001 ARG A 854 Details of bonding type rmsd hydrogen bonds : bond 0.14991 ( 391) hydrogen bonds : angle 6.38825 ( 1080) covalent geometry : bond 0.00274 (12055) covalent geometry : angle 0.55967 (16429) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 235 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.6350 (mpp) cc_final: 0.5389 (tpt) REVERT: A 428 LEU cc_start: 0.7822 (mt) cc_final: 0.7057 (pp) REVERT: A 548 ASP cc_start: 0.6717 (m-30) cc_final: 0.6342 (p0) REVERT: A 699 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6945 (ttpp) REVERT: C 159 ARG cc_start: 0.8148 (mtp-110) cc_final: 0.7867 (ttp-110) REVERT: C 222 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7661 (mp0) outliers start: 7 outliers final: 1 residues processed: 240 average time/residue: 0.3003 time to fit residues: 97.8514 Evaluate side-chains 127 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 699 LYS Chi-restraints excluded: chain B residue 183 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.0370 chunk 117 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 40 optimal weight: 0.0370 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 GLN B 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.154079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.110874 restraints weight = 16287.278| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.21 r_work: 0.3203 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12055 Z= 0.115 Angle : 0.545 7.167 16429 Z= 0.279 Chirality : 0.044 0.149 1865 Planarity : 0.004 0.040 2127 Dihedral : 4.277 49.812 1679 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.89 % Allowed : 18.79 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % 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: -0.36 (0.22), residues: 1536 helix: 0.88 (0.35), residues: 240 sheet: 0.28 (0.25), residues: 455 loop : -0.85 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 257 HIS 0.004 0.001 HIS A 561 PHE 0.022 0.001 PHE B 322 TYR 0.012 0.001 TYR A 254 ARG 0.005 0.001 ARG A 467 Details of bonding type rmsd hydrogen bonds : bond 0.03983 ( 391) hydrogen bonds : angle 4.89197 ( 1080) covalent geometry : bond 0.00262 (12055) covalent geometry : angle 0.54451 (16429) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: A 85 GLN cc_start: 0.7761 (mt0) cc_final: 0.7356 (mt0) REVERT: A 152 ASN cc_start: 0.6757 (m-40) cc_final: 0.6087 (m-40) REVERT: A 185 ARG cc_start: 0.7799 (ptm160) cc_final: 0.7530 (ptm160) REVERT: A 428 LEU cc_start: 0.7841 (mt) cc_final: 0.7051 (pp) REVERT: A 544 GLN cc_start: 0.7769 (mt0) cc_final: 0.7480 (mp10) REVERT: A 548 ASP cc_start: 0.6803 (m-30) cc_final: 0.6242 (p0) REVERT: B 132 TRP cc_start: 0.6761 (OUTLIER) cc_final: 0.6402 (m-90) REVERT: B 387 ASP cc_start: 0.8466 (t0) cc_final: 0.8169 (t70) REVERT: B 401 LYS cc_start: 0.8232 (tptt) cc_final: 0.7449 (tttt) REVERT: C 62 TYR cc_start: 0.6421 (OUTLIER) cc_final: 0.5663 (p90) REVERT: C 159 ARG cc_start: 0.8327 (mtp-110) cc_final: 0.7897 (ttp-110) REVERT: C 222 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7531 (mp0) outliers start: 34 outliers final: 21 residues processed: 163 average time/residue: 0.2401 time to fit residues: 56.9633 Evaluate side-chains 135 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 157 ARG Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 305 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 5 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 99 optimal weight: 0.1980 chunk 19 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS A 869 ASN B 472 GLN C 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.150714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108510 restraints weight = 16530.322| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.03 r_work: 0.3185 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12055 Z= 0.205 Angle : 0.609 6.419 16429 Z= 0.311 Chirality : 0.048 0.255 1865 Planarity : 0.005 0.044 2127 Dihedral : 4.404 36.931 1675 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.68 % Allowed : 19.73 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % 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: -0.55 (0.22), residues: 1536 helix: 0.68 (0.35), residues: 238 sheet: -0.04 (0.24), residues: 466 loop : -0.83 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 257 HIS 0.009 0.001 HIS A 442 PHE 0.019 0.002 PHE A 580 TYR 0.019 0.002 TYR A 351 ARG 0.006 0.001 ARG A 563 Details of bonding type rmsd hydrogen bonds : bond 0.04493 ( 391) hydrogen bonds : angle 5.06061 ( 1080) covalent geometry : bond 0.00498 (12055) covalent geometry : angle 0.60914 (16429) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 122 time to evaluate : 1.368 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8279 (tpt) cc_final: 0.7914 (mtt) REVERT: A 85 GLN cc_start: 0.7835 (mt0) cc_final: 0.7408 (mt0) REVERT: A 548 ASP cc_start: 0.6690 (m-30) cc_final: 0.6243 (p0) REVERT: A 919 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7276 (tm-30) REVERT: B 169 TYR cc_start: 0.6024 (OUTLIER) cc_final: 0.5145 (m-10) REVERT: B 387 ASP cc_start: 0.8495 (t0) cc_final: 0.8171 (t70) REVERT: B 479 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.9031 (mp) REVERT: C 159 ARG cc_start: 0.8321 (mtp-110) cc_final: 0.7876 (ttp-110) REVERT: C 222 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7688 (mp0) outliers start: 55 outliers final: 37 residues processed: 166 average time/residue: 0.2318 time to fit residues: 56.2319 Evaluate side-chains 147 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 802 SER Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 919 GLU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 157 ARG Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 305 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 154 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 115 optimal weight: 0.0010 chunk 124 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.155488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.112756 restraints weight = 16291.897| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.05 r_work: 0.3223 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12055 Z= 0.099 Angle : 0.513 7.823 16429 Z= 0.259 Chirality : 0.044 0.172 1865 Planarity : 0.004 0.077 2127 Dihedral : 4.049 36.771 1675 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.23 % Allowed : 20.66 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % 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: -0.27 (0.22), residues: 1536 helix: 1.06 (0.35), residues: 238 sheet: 0.05 (0.25), residues: 450 loop : -0.63 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 257 HIS 0.003 0.001 HIS A 561 PHE 0.018 0.001 PHE B 322 TYR 0.008 0.001 TYR A 275 ARG 0.005 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 391) hydrogen bonds : angle 4.63507 ( 1080) covalent geometry : bond 0.00225 (12055) covalent geometry : angle 0.51273 (16429) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.8165 (tpt) cc_final: 0.7878 (mtt) REVERT: A 85 GLN cc_start: 0.7834 (mt0) cc_final: 0.7469 (mt0) REVERT: A 176 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8060 (pt0) REVERT: A 544 GLN cc_start: 0.7727 (mt0) cc_final: 0.7478 (mp10) REVERT: A 548 ASP cc_start: 0.6764 (m-30) cc_final: 0.6226 (p0) REVERT: A 562 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7936 (pt0) REVERT: B 387 ASP cc_start: 0.8456 (t0) cc_final: 0.8106 (t70) REVERT: C 62 TYR cc_start: 0.6390 (OUTLIER) cc_final: 0.5601 (p90) REVERT: C 159 ARG cc_start: 0.8372 (mtp-110) cc_final: 0.7891 (ttp-110) REVERT: C 222 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7683 (mp0) outliers start: 38 outliers final: 28 residues processed: 147 average time/residue: 0.2329 time to fit residues: 49.9309 Evaluate side-chains 134 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 157 ARG Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 305 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 29 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 18 optimal weight: 0.0870 chunk 80 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS ** A 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 869 ASN ** A 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.150055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.108004 restraints weight = 16484.922| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.01 r_work: 0.3168 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12055 Z= 0.202 Angle : 0.596 7.631 16429 Z= 0.302 Chirality : 0.047 0.164 1865 Planarity : 0.005 0.060 2127 Dihedral : 4.380 38.161 1675 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.68 % Allowed : 19.64 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % 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: -0.52 (0.22), residues: 1536 helix: 0.97 (0.35), residues: 238 sheet: -0.12 (0.25), residues: 456 loop : -0.82 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 238 HIS 0.007 0.001 HIS A 442 PHE 0.019 0.002 PHE A 580 TYR 0.014 0.002 TYR C 172 ARG 0.004 0.000 ARG A 620 Details of bonding type rmsd hydrogen bonds : bond 0.04219 ( 391) hydrogen bonds : angle 4.87591 ( 1080) covalent geometry : bond 0.00491 (12055) covalent geometry : angle 0.59627 (16429) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 115 time to evaluate : 1.438 Fit side-chains REVERT: A 67 MET cc_start: 0.8187 (tpt) cc_final: 0.7916 (mtt) REVERT: A 85 GLN cc_start: 0.7858 (mt0) cc_final: 0.7402 (mt0) REVERT: A 401 TRP cc_start: 0.7914 (t-100) cc_final: 0.7705 (t-100) REVERT: A 548 ASP cc_start: 0.6688 (m-30) cc_final: 0.6193 (p0) REVERT: A 562 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7925 (pt0) REVERT: A 698 ARG cc_start: 0.6323 (OUTLIER) cc_final: 0.4779 (mmt-90) REVERT: A 919 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7253 (tm-30) REVERT: B 169 TYR cc_start: 0.5973 (OUTLIER) cc_final: 0.5103 (m-10) REVERT: B 387 ASP cc_start: 0.8464 (t0) cc_final: 0.8095 (t0) REVERT: C 159 ARG cc_start: 0.8392 (mtp-110) cc_final: 0.7941 (ttp-110) REVERT: C 222 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7708 (mp0) outliers start: 55 outliers final: 42 residues processed: 159 average time/residue: 0.2397 time to fit residues: 55.0922 Evaluate side-chains 153 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 107 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 802 SER Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 919 GLU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 157 ARG Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 305 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 99 optimal weight: 30.0000 chunk 98 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 134 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.152170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.110167 restraints weight = 16589.750| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.00 r_work: 0.3187 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12055 Z= 0.149 Angle : 0.544 7.659 16429 Z= 0.274 Chirality : 0.045 0.151 1865 Planarity : 0.004 0.055 2127 Dihedral : 4.235 39.455 1675 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.51 % Allowed : 20.24 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % 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: -0.52 (0.22), residues: 1536 helix: 0.70 (0.34), residues: 256 sheet: -0.07 (0.25), residues: 454 loop : -0.80 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 238 HIS 0.004 0.001 HIS A 29 PHE 0.016 0.002 PHE A 300 TYR 0.010 0.001 TYR C 172 ARG 0.003 0.000 ARG A 620 Details of bonding type rmsd hydrogen bonds : bond 0.03745 ( 391) hydrogen bonds : angle 4.70534 ( 1080) covalent geometry : bond 0.00360 (12055) covalent geometry : angle 0.54390 (16429) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 107 time to evaluate : 1.412 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8166 (tpt) cc_final: 0.7917 (mtt) REVERT: A 85 GLN cc_start: 0.7882 (mt0) cc_final: 0.7440 (mt0) REVERT: A 157 GLN cc_start: 0.7517 (tt0) cc_final: 0.7063 (tt0) REVERT: A 548 ASP cc_start: 0.6711 (m-30) cc_final: 0.6191 (p0) REVERT: A 562 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7940 (pt0) REVERT: A 574 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: A 698 ARG cc_start: 0.6321 (OUTLIER) cc_final: 0.4819 (mmt-90) REVERT: A 780 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8077 (mt) REVERT: A 919 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7115 (tm-30) REVERT: B 328 LEU cc_start: 0.7928 (mt) cc_final: 0.7624 (mt) REVERT: B 387 ASP cc_start: 0.8451 (t0) cc_final: 0.8098 (t0) REVERT: C 222 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7742 (mp0) outliers start: 53 outliers final: 41 residues processed: 152 average time/residue: 0.2768 time to fit residues: 61.7426 Evaluate side-chains 147 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 101 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 919 GLU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 157 ARG Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 305 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 20 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 GLN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.150796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108717 restraints weight = 16694.920| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.02 r_work: 0.3171 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12055 Z= 0.181 Angle : 0.571 7.635 16429 Z= 0.289 Chirality : 0.046 0.153 1865 Planarity : 0.004 0.053 2127 Dihedral : 4.364 40.391 1675 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.59 % Allowed : 19.98 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % 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: -0.58 (0.22), residues: 1536 helix: 0.76 (0.34), residues: 250 sheet: -0.20 (0.25), residues: 462 loop : -0.81 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 132 HIS 0.005 0.001 HIS A 29 PHE 0.017 0.002 PHE A 580 TYR 0.012 0.001 TYR A 351 ARG 0.003 0.000 ARG A 844 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 391) hydrogen bonds : angle 4.80074 ( 1080) covalent geometry : bond 0.00439 (12055) covalent geometry : angle 0.57093 (16429) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 118 time to evaluate : 1.256 Fit side-chains REVERT: A 67 MET cc_start: 0.8166 (tpt) cc_final: 0.7858 (mtt) REVERT: A 85 GLN cc_start: 0.7899 (mt0) cc_final: 0.7431 (mt0) REVERT: A 157 GLN cc_start: 0.7552 (tt0) cc_final: 0.7047 (tt0) REVERT: A 548 ASP cc_start: 0.6689 (m-30) cc_final: 0.6201 (p0) REVERT: A 562 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7936 (pt0) REVERT: A 574 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: A 698 ARG cc_start: 0.6329 (OUTLIER) cc_final: 0.4803 (mmt-90) REVERT: A 780 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8071 (mt) REVERT: A 919 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7365 (tp30) REVERT: B 169 TYR cc_start: 0.6006 (OUTLIER) cc_final: 0.5046 (m-10) REVERT: B 387 ASP cc_start: 0.8469 (t0) cc_final: 0.8106 (t0) REVERT: C 222 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7603 (mp0) outliers start: 54 outliers final: 45 residues processed: 160 average time/residue: 0.2395 time to fit residues: 55.0628 Evaluate side-chains 157 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 106 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 802 SER Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 919 GLU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 169 TYR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 157 ARG Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 305 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 12 optimal weight: 0.4980 chunk 9 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 111 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.153449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.111163 restraints weight = 16462.360| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.01 r_work: 0.3208 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12055 Z= 0.112 Angle : 0.515 7.719 16429 Z= 0.261 Chirality : 0.044 0.153 1865 Planarity : 0.004 0.050 2127 Dihedral : 4.109 40.624 1675 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.57 % Allowed : 21.09 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % 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: -0.41 (0.22), residues: 1536 helix: 0.77 (0.34), residues: 257 sheet: -0.02 (0.25), residues: 451 loop : -0.70 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 132 HIS 0.003 0.001 HIS A 29 PHE 0.016 0.001 PHE B 322 TYR 0.008 0.001 TYR A 911 ARG 0.003 0.000 ARG C 174 Details of bonding type rmsd hydrogen bonds : bond 0.03404 ( 391) hydrogen bonds : angle 4.56257 ( 1080) covalent geometry : bond 0.00265 (12055) covalent geometry : angle 0.51522 (16429) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 115 time to evaluate : 1.369 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8135 (tpt) cc_final: 0.7824 (mtt) REVERT: A 85 GLN cc_start: 0.7882 (mt0) cc_final: 0.7440 (mt0) REVERT: A 157 GLN cc_start: 0.7416 (tt0) cc_final: 0.6993 (tt0) REVERT: A 548 ASP cc_start: 0.6748 (m-30) cc_final: 0.6213 (p0) REVERT: A 562 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7957 (pt0) REVERT: A 574 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7831 (tt0) REVERT: A 698 ARG cc_start: 0.6347 (OUTLIER) cc_final: 0.4762 (mmt-90) REVERT: B 308 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7426 (mt0) REVERT: B 387 ASP cc_start: 0.8426 (t0) cc_final: 0.8086 (t0) REVERT: C 222 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7640 (mp0) outliers start: 42 outliers final: 31 residues processed: 148 average time/residue: 0.3171 time to fit residues: 68.1676 Evaluate side-chains 142 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 157 ARG Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 305 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 138 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 11 optimal weight: 0.0470 chunk 65 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 869 ASN B 383 ASN ** C 48 GLN ** 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 = 0.3918 r_free = 0.3918 target = 0.154291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113720 restraints weight = 16408.473| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.08 r_work: 0.3217 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12055 Z= 0.103 Angle : 0.519 11.080 16429 Z= 0.258 Chirality : 0.044 0.164 1865 Planarity : 0.004 0.078 2127 Dihedral : 3.786 18.561 1673 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.23 % Allowed : 21.68 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % 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: -0.36 (0.22), residues: 1536 helix: 0.70 (0.34), residues: 263 sheet: 0.04 (0.25), residues: 451 loop : -0.66 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 238 HIS 0.003 0.001 HIS B 370 PHE 0.025 0.001 PHE B 582 TYR 0.008 0.001 TYR A 911 ARG 0.003 0.000 ARG C 174 Details of bonding type rmsd hydrogen bonds : bond 0.03302 ( 391) hydrogen bonds : angle 4.45199 ( 1080) covalent geometry : bond 0.00242 (12055) covalent geometry : angle 0.51908 (16429) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 3.223 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8114 (tpt) cc_final: 0.7795 (mtt) REVERT: A 85 GLN cc_start: 0.7845 (mt0) cc_final: 0.7447 (mt0) REVERT: A 157 GLN cc_start: 0.7498 (tt0) cc_final: 0.6992 (tt0) REVERT: A 548 ASP cc_start: 0.6733 (m-30) cc_final: 0.6202 (p0) REVERT: A 562 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7969 (pt0) REVERT: A 698 ARG cc_start: 0.6336 (OUTLIER) cc_final: 0.4760 (mmt-90) REVERT: B 308 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7455 (mt0) REVERT: B 387 ASP cc_start: 0.8402 (t0) cc_final: 0.8093 (t0) REVERT: C 222 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7859 (mp0) REVERT: C 299 GLU cc_start: 0.7325 (mt-10) cc_final: 0.7095 (mt-10) outliers start: 38 outliers final: 30 residues processed: 143 average time/residue: 0.4399 time to fit residues: 92.3087 Evaluate side-chains 140 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 157 ARG Chi-restraints excluded: chain C residue 173 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 86 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 128 optimal weight: 0.5980 chunk 129 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.153574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.111045 restraints weight = 16391.491| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.06 r_work: 0.3204 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12055 Z= 0.107 Angle : 0.521 9.943 16429 Z= 0.260 Chirality : 0.044 0.158 1865 Planarity : 0.004 0.073 2127 Dihedral : 3.765 19.809 1673 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.32 % Allowed : 21.68 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % 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: -0.29 (0.22), residues: 1536 helix: 0.72 (0.34), residues: 262 sheet: 0.12 (0.25), residues: 450 loop : -0.63 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 238 HIS 0.003 0.001 HIS B 370 PHE 0.018 0.001 PHE B 330 TYR 0.008 0.001 TYR A 275 ARG 0.003 0.000 ARG C 247 Details of bonding type rmsd hydrogen bonds : bond 0.03276 ( 391) hydrogen bonds : angle 4.40821 ( 1080) covalent geometry : bond 0.00257 (12055) covalent geometry : angle 0.52057 (16429) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 1.391 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8125 (tpt) cc_final: 0.7791 (mtt) REVERT: A 85 GLN cc_start: 0.7850 (mt0) cc_final: 0.7455 (mt0) REVERT: A 157 GLN cc_start: 0.7505 (tt0) cc_final: 0.6973 (tt0) REVERT: A 548 ASP cc_start: 0.6779 (m-30) cc_final: 0.6203 (p0) REVERT: A 562 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7963 (pt0) REVERT: A 698 ARG cc_start: 0.6339 (OUTLIER) cc_final: 0.4769 (mmt-90) REVERT: B 98 ASP cc_start: 0.6188 (t0) cc_final: 0.5953 (t0) REVERT: B 308 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7436 (mt0) REVERT: B 387 ASP cc_start: 0.8387 (t0) cc_final: 0.8094 (t0) REVERT: B 529 MET cc_start: 0.6846 (mmt) cc_final: 0.6636 (tpp) REVERT: C 222 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7869 (mp0) REVERT: C 299 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7072 (mt-10) outliers start: 39 outliers final: 33 residues processed: 143 average time/residue: 0.2582 time to fit residues: 53.2529 Evaluate side-chains 145 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 157 ARG Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 298 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 5 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 149 optimal weight: 0.0470 chunk 118 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 869 ASN B 173 ASN ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.153730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111704 restraints weight = 16350.662| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.03 r_work: 0.3212 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12055 Z= 0.105 Angle : 0.521 10.182 16429 Z= 0.258 Chirality : 0.044 0.156 1865 Planarity : 0.004 0.070 2127 Dihedral : 3.738 20.867 1673 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.49 % Allowed : 21.43 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % 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: -0.26 (0.22), residues: 1536 helix: 0.78 (0.34), residues: 261 sheet: 0.14 (0.25), residues: 448 loop : -0.62 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 132 HIS 0.003 0.001 HIS B 370 PHE 0.014 0.001 PHE B 322 TYR 0.009 0.001 TYR A 717 ARG 0.004 0.000 ARG C 247 Details of bonding type rmsd hydrogen bonds : bond 0.03217 ( 391) hydrogen bonds : angle 4.39491 ( 1080) covalent geometry : bond 0.00250 (12055) covalent geometry : angle 0.52063 (16429) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6449.00 seconds wall clock time: 114 minutes 17.39 seconds (6857.39 seconds total)