Starting phenix.real_space_refine on Wed Sep 17 22:27:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ejl_48104/09_2025/9ejl_48104_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ejl_48104/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ejl_48104/09_2025/9ejl_48104_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ejl_48104/09_2025/9ejl_48104_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ejl_48104/09_2025/9ejl_48104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ejl_48104/09_2025/9ejl_48104.map" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 13, 'GLU:plan': 20, 'ASP:plan': 8, 'ASN:plan1': 1, 'TYR:plan': 1, 'GLN:plan1': 1} 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: {'GLU:plan': 18, 'ASP:plan': 18, 'GLN:plan1': 4, 'ARG:plan': 12, 'TYR:plan': 1, 'HIS:plan': 2, 'ASN:plan1': 2, 'TPO:plan-1': 2, 'PHE:plan': 1} 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: {'GLU:plan': 8, 'PHE:plan': 1, 'ASP:plan': 6, 'HIS:plan': 1, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 84 Time building chain proxies: 2.82, per 1000 atoms: 0.24 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: 0.93 Conformation dependent library (CDL) restraints added in 564.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.50 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: 2.28 Time building geometry restraints manager: 1.25 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: 0.010 Normalize map: mean=0, sd=1: 8.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.660 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.840 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (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 ARG 0.025 0.001 ARG A 854 TYR 0.016 0.001 TYR A 254 PHE 0.019 0.001 PHE B 148 TRP 0.038 0.002 TRP B 132 HIS 0.005 0.001 HIS A 561 Details of bonding type rmsd covalent geometry : bond 0.00274 (12055) covalent geometry : angle 0.55967 (16429) hydrogen bonds : bond 0.14991 ( 391) hydrogen bonds : angle 6.38825 ( 1080) *********************** 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 : 0.447 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: 0.1320 time to fit residues: 43.0396 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 : 0.393 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.0370 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.0670 chunk 149 optimal weight: 7.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- 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 = 0.3877 r_free = 0.3877 target = 0.151424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.108474 restraints weight = 16378.095| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.17 r_work: 0.3169 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12055 Z= 0.157 Angle : 0.578 6.816 16429 Z= 0.296 Chirality : 0.046 0.158 1865 Planarity : 0.005 0.043 2127 Dihedral : 4.384 40.888 1679 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.32 % Allowed : 18.96 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.22), residues: 1536 helix: 0.89 (0.35), residues: 234 sheet: 0.11 (0.25), residues: 461 loop : -0.92 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 620 TYR 0.017 0.001 TYR C 172 PHE 0.022 0.002 PHE B 322 TRP 0.018 0.002 TRP A 257 HIS 0.007 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00375 (12055) covalent geometry : angle 0.57778 (16429) hydrogen bonds : bond 0.04221 ( 391) hydrogen bonds : angle 4.97753 ( 1080) *********************** 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 175 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 85 GLN cc_start: 0.7799 (mt0) cc_final: 0.7383 (mt0) REVERT: A 152 ASN cc_start: 0.6799 (m-40) cc_final: 0.6140 (m-40) REVERT: A 185 ARG cc_start: 0.7806 (ptm160) cc_final: 0.7551 (ptm160) REVERT: A 428 LEU cc_start: 0.7860 (mt) cc_final: 0.7076 (pp) REVERT: A 544 GLN cc_start: 0.7787 (mt0) cc_final: 0.7525 (mp10) REVERT: A 548 ASP cc_start: 0.6815 (m-30) cc_final: 0.6252 (p0) REVERT: A 919 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7198 (tm-30) REVERT: B 169 TYR cc_start: 0.6099 (OUTLIER) cc_final: 0.4998 (m-10) REVERT: B 387 ASP cc_start: 0.8508 (t0) cc_final: 0.8166 (t70) REVERT: C 62 TYR cc_start: 0.6434 (OUTLIER) cc_final: 0.5715 (p90) REVERT: C 159 ARG cc_start: 0.8342 (mtp-110) cc_final: 0.7901 (ttp-110) REVERT: C 222 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7623 (mp0) outliers start: 39 outliers final: 24 residues processed: 166 average time/residue: 0.1037 time to fit residues: 24.8959 Evaluate side-chains 137 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 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 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 400 CYS 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 58 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS ** A 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3850 r_free = 0.3850 target = 0.148638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106253 restraints weight = 16711.444| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.06 r_work: 0.3142 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12055 Z= 0.251 Angle : 0.651 7.096 16429 Z= 0.335 Chirality : 0.049 0.211 1865 Planarity : 0.005 0.049 2127 Dihedral : 4.663 36.507 1675 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.93 % Allowed : 19.13 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.22), residues: 1536 helix: 0.53 (0.34), residues: 238 sheet: -0.29 (0.24), residues: 480 loop : -1.02 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 620 TYR 0.020 0.002 TYR C 172 PHE 0.021 0.002 PHE A 580 TRP 0.027 0.002 TRP A 257 HIS 0.009 0.002 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00611 (12055) covalent geometry : angle 0.65101 (16429) hydrogen bonds : bond 0.04807 ( 391) hydrogen bonds : angle 5.28045 ( 1080) *********************** 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 173 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 115 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8288 (tpt) cc_final: 0.8062 (mtm) REVERT: A 85 GLN cc_start: 0.7854 (mt0) cc_final: 0.7389 (mt0) REVERT: A 177 ARG cc_start: 0.7998 (mmm160) cc_final: 0.7797 (mmp-170) REVERT: A 548 ASP cc_start: 0.6741 (m-30) cc_final: 0.6202 (p0) REVERT: A 562 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7896 (pt0) REVERT: B 169 TYR cc_start: 0.5979 (OUTLIER) cc_final: 0.5098 (m-10) REVERT: B 387 ASP cc_start: 0.8525 (t0) cc_final: 0.8141 (t0) REVERT: C 159 ARG cc_start: 0.8389 (mtp-110) cc_final: 0.7946 (ttp-110) REVERT: C 222 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7691 (mp0) outliers start: 58 outliers final: 40 residues processed: 165 average time/residue: 0.1034 time to fit residues: 24.8102 Evaluate side-chains 147 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 105 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 272 LEU Chi-restraints excluded: chain A residue 353 LEU 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 553 GLN Chi-restraints excluded: chain A residue 562 GLU 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 760 VAL Chi-restraints excluded: chain A residue 802 SER 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 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 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 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 205 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 97 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.150581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.108186 restraints weight = 16479.797| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.06 r_work: 0.3168 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12055 Z= 0.143 Angle : 0.549 7.986 16429 Z= 0.279 Chirality : 0.045 0.160 1865 Planarity : 0.004 0.048 2127 Dihedral : 4.355 38.315 1675 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.91 % Allowed : 20.32 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.22), residues: 1536 helix: 0.87 (0.35), residues: 238 sheet: -0.18 (0.25), residues: 457 loop : -0.94 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 174 TYR 0.011 0.001 TYR C 172 PHE 0.020 0.002 PHE B 579 TRP 0.026 0.002 TRP A 401 HIS 0.004 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00343 (12055) covalent geometry : angle 0.54878 (16429) hydrogen bonds : bond 0.03923 ( 391) hydrogen bonds : angle 4.89535 ( 1080) *********************** 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 157 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 111 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8236 (tpt) cc_final: 0.7946 (mtt) REVERT: A 85 GLN cc_start: 0.7885 (mt0) cc_final: 0.7430 (mt0) REVERT: A 548 ASP cc_start: 0.6817 (m-30) cc_final: 0.6253 (p0) REVERT: A 780 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8098 (mt) REVERT: B 169 TYR cc_start: 0.5960 (OUTLIER) cc_final: 0.5066 (m-10) REVERT: B 387 ASP cc_start: 0.8474 (t0) cc_final: 0.8097 (t0) REVERT: C 159 ARG cc_start: 0.8390 (mtp-110) cc_final: 0.7929 (ttp-110) REVERT: C 222 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7675 (mp0) outliers start: 46 outliers final: 33 residues processed: 149 average time/residue: 0.1111 time to fit residues: 23.7165 Evaluate side-chains 138 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 103 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 246 VAL Chi-restraints excluded: chain A residue 342 ASP 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 598 SER 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 780 LEU Chi-restraints excluded: chain A residue 802 SER 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 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 410 THR 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 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 36 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 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** B 472 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.147573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.107028 restraints weight = 16753.186| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.11 r_work: 0.3125 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 12055 Z= 0.253 Angle : 0.636 7.338 16429 Z= 0.326 Chirality : 0.048 0.166 1865 Planarity : 0.005 0.051 2127 Dihedral : 4.715 39.869 1675 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.93 % Allowed : 19.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.22), residues: 1536 helix: 0.50 (0.34), residues: 248 sheet: -0.43 (0.25), residues: 455 loop : -1.04 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 620 TYR 0.016 0.002 TYR A 351 PHE 0.021 0.002 PHE A 580 TRP 0.039 0.002 TRP A 401 HIS 0.008 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00615 (12055) covalent geometry : angle 0.63564 (16429) hydrogen bonds : bond 0.04685 ( 391) hydrogen bonds : angle 5.18966 ( 1080) *********************** 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 181 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 123 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 24 ASN cc_start: 0.8867 (t0) cc_final: 0.8241 (t0) REVERT: A 67 MET cc_start: 0.8248 (tpt) cc_final: 0.7960 (mtt) REVERT: A 157 GLN cc_start: 0.7544 (tt0) cc_final: 0.7163 (tt0) REVERT: A 548 ASP cc_start: 0.6732 (m-30) cc_final: 0.6211 (p0) REVERT: A 562 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7934 (pt0) REVERT: A 698 ARG cc_start: 0.6183 (OUTLIER) cc_final: 0.4758 (mmt-90) REVERT: B 169 TYR cc_start: 0.6000 (OUTLIER) cc_final: 0.5154 (m-10) REVERT: C 222 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7550 (mp0) outliers start: 58 outliers final: 48 residues processed: 168 average time/residue: 0.1125 time to fit residues: 27.3216 Evaluate side-chains 165 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 114 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 272 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 332 VAL 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 553 GLN 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 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 812 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 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 410 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 472 GLN 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 46 optimal weight: 0.6980 chunk 17 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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** ** A 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.148567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106410 restraints weight = 16674.012| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.03 r_work: 0.3137 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12055 Z= 0.228 Angle : 0.619 8.146 16429 Z= 0.316 Chirality : 0.048 0.167 1865 Planarity : 0.005 0.052 2127 Dihedral : 4.711 41.278 1675 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.19 % Allowed : 19.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.21), residues: 1536 helix: 0.47 (0.34), residues: 248 sheet: -0.50 (0.25), residues: 456 loop : -1.10 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 174 TYR 0.014 0.002 TYR C 172 PHE 0.018 0.002 PHE A 580 TRP 0.052 0.002 TRP A 401 HIS 0.007 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00558 (12055) covalent geometry : angle 0.61880 (16429) hydrogen bonds : bond 0.04514 ( 391) hydrogen bonds : angle 5.13981 ( 1080) *********************** 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 182 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 121 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8194 (tpt) cc_final: 0.7968 (mtt) REVERT: A 157 GLN cc_start: 0.7509 (tt0) cc_final: 0.7116 (tt0) REVERT: A 176 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8358 (pt0) REVERT: A 548 ASP cc_start: 0.6757 (m-30) cc_final: 0.6219 (p0) REVERT: A 562 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7941 (pt0) REVERT: A 698 ARG cc_start: 0.6207 (OUTLIER) cc_final: 0.4785 (mmt-90) REVERT: A 932 ARG cc_start: 0.6078 (OUTLIER) cc_final: 0.5433 (ptm160) REVERT: B 169 TYR cc_start: 0.6001 (OUTLIER) cc_final: 0.5120 (m-10) REVERT: B 308 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7452 (mt0) REVERT: C 222 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7570 (mp0) outliers start: 61 outliers final: 48 residues processed: 167 average time/residue: 0.1080 time to fit residues: 26.1373 Evaluate side-chains 167 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 113 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 332 VAL 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 463 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 553 GLN 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 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 914 SER Chi-restraints excluded: chain A residue 932 ARG 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 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 B residue 420 ILE Chi-restraints excluded: chain B residue 446 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 125 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 78 optimal weight: 0.2980 chunk 139 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- 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 232 GLN ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 GLN B 391 HIS ** 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 = 0.3839 r_free = 0.3839 target = 0.147667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105720 restraints weight = 16685.673| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.04 r_work: 0.3132 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12055 Z= 0.221 Angle : 0.614 6.806 16429 Z= 0.314 Chirality : 0.047 0.159 1865 Planarity : 0.005 0.054 2127 Dihedral : 4.708 42.250 1675 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.19 % Allowed : 19.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.21), residues: 1536 helix: 0.48 (0.34), residues: 248 sheet: -0.57 (0.24), residues: 467 loop : -1.12 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 174 TYR 0.013 0.002 TYR C 172 PHE 0.017 0.002 PHE A 580 TRP 0.057 0.002 TRP A 401 HIS 0.006 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00539 (12055) covalent geometry : angle 0.61355 (16429) hydrogen bonds : bond 0.04477 ( 391) hydrogen bonds : angle 5.12294 ( 1080) *********************** 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 182 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 121 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 24 ASN cc_start: 0.8865 (t0) cc_final: 0.8202 (t0) REVERT: A 67 MET cc_start: 0.8194 (tpt) cc_final: 0.7920 (mtt) REVERT: A 157 GLN cc_start: 0.7489 (tt0) cc_final: 0.7067 (tt0) REVERT: A 548 ASP cc_start: 0.6770 (m-30) cc_final: 0.6222 (p0) REVERT: A 562 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7955 (pt0) REVERT: A 698 ARG cc_start: 0.6218 (OUTLIER) cc_final: 0.4801 (mmt-90) REVERT: A 932 ARG cc_start: 0.6056 (OUTLIER) cc_final: 0.5470 (ptm160) REVERT: B 169 TYR cc_start: 0.6025 (OUTLIER) cc_final: 0.5134 (m-10) REVERT: B 308 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7400 (mt0) REVERT: B 361 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6015 (tt0) REVERT: C 222 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7598 (mp0) outliers start: 61 outliers final: 51 residues processed: 167 average time/residue: 0.1109 time to fit residues: 26.5733 Evaluate side-chains 168 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 111 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 272 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 332 VAL 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 463 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 553 GLN 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 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 836 THR 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 932 ARG 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 256 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 361 GLU 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 446 MET 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 75 ASP Chi-restraints excluded: chain C residue 157 ARG 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 28 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 68 optimal weight: 0.0770 chunk 48 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 132 optimal weight: 0.5980 chunk 106 optimal weight: 9.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- 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 869 ASN ** 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 = 0.3868 r_free = 0.3868 target = 0.150157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.108169 restraints weight = 16439.848| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.05 r_work: 0.3170 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12055 Z= 0.119 Angle : 0.541 8.126 16429 Z= 0.274 Chirality : 0.045 0.150 1865 Planarity : 0.004 0.053 2127 Dihedral : 4.354 42.372 1675 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.00 % Allowed : 21.17 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.22), residues: 1536 helix: 0.61 (0.34), residues: 254 sheet: -0.40 (0.24), residues: 466 loop : -0.95 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 174 TYR 0.010 0.001 TYR A 911 PHE 0.019 0.002 PHE B 579 TRP 0.046 0.002 TRP A 401 HIS 0.003 0.001 HIS B 370 Details of bonding type rmsd covalent geometry : bond 0.00284 (12055) covalent geometry : angle 0.54092 (16429) hydrogen bonds : bond 0.03702 ( 391) hydrogen bonds : angle 4.76060 ( 1080) *********************** 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 167 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 120 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ASN cc_start: 0.8816 (t0) cc_final: 0.8166 (t0) REVERT: A 67 MET cc_start: 0.8144 (tpt) cc_final: 0.7896 (mtt) REVERT: A 157 GLN cc_start: 0.7435 (tt0) cc_final: 0.7081 (tt0) REVERT: A 548 ASP cc_start: 0.6833 (m-30) cc_final: 0.6215 (p0) REVERT: A 562 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7968 (pt0) REVERT: A 698 ARG cc_start: 0.6257 (OUTLIER) cc_final: 0.4875 (mmt-90) REVERT: A 780 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7998 (mt) REVERT: B 169 TYR cc_start: 0.6031 (OUTLIER) cc_final: 0.5071 (m-10) REVERT: B 308 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7430 (mt0) REVERT: C 222 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7599 (mp0) outliers start: 47 outliers final: 34 residues processed: 158 average time/residue: 0.1107 time to fit residues: 25.4936 Evaluate side-chains 152 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 308 SER 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 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 780 LEU Chi-restraints excluded: chain A residue 802 SER Chi-restraints excluded: chain A residue 870 LEU 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 153 HIS Chi-restraints excluded: chain B residue 169 TYR 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 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 298 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 134 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 139 optimal weight: 0.0040 chunk 23 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- 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** ** 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 = 0.3849 r_free = 0.3849 target = 0.148448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106161 restraints weight = 16598.926| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.14 r_work: 0.3135 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12055 Z= 0.169 Angle : 0.571 12.191 16429 Z= 0.291 Chirality : 0.046 0.154 1865 Planarity : 0.005 0.051 2127 Dihedral : 4.226 19.690 1673 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.91 % Allowed : 21.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.22), residues: 1536 helix: 0.58 (0.34), residues: 254 sheet: -0.44 (0.25), residues: 466 loop : -0.98 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 174 TYR 0.011 0.001 TYR C 172 PHE 0.018 0.002 PHE B 579 TRP 0.040 0.002 TRP A 401 HIS 0.004 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00409 (12055) covalent geometry : angle 0.57135 (16429) hydrogen bonds : bond 0.04066 ( 391) hydrogen bonds : angle 4.81438 ( 1080) *********************** 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 165 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 119 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ASN cc_start: 0.8855 (t0) cc_final: 0.8237 (t0) REVERT: A 67 MET cc_start: 0.8127 (tpt) cc_final: 0.7892 (mtt) REVERT: A 157 GLN cc_start: 0.7456 (tt0) cc_final: 0.6967 (tt0) REVERT: A 548 ASP cc_start: 0.6776 (m-30) cc_final: 0.6220 (p0) REVERT: A 562 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7988 (pt0) REVERT: A 698 ARG cc_start: 0.6337 (OUTLIER) cc_final: 0.4916 (mmt-90) REVERT: B 169 TYR cc_start: 0.6045 (OUTLIER) cc_final: 0.5115 (m-10) REVERT: B 308 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7465 (mt0) REVERT: C 222 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7642 (mp0) outliers start: 46 outliers final: 41 residues processed: 155 average time/residue: 0.1160 time to fit residues: 26.1806 Evaluate side-chains 161 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 116 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 272 LEU Chi-restraints excluded: chain A residue 308 SER 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 553 GLN 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 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 812 LEU Chi-restraints excluded: chain A residue 870 LEU 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 153 HIS Chi-restraints excluded: chain B residue 169 TYR 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 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 298 ILE Chi-restraints excluded: chain C residue 305 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.0020 chunk 116 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 16 optimal weight: 0.0770 chunk 35 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 118 optimal weight: 0.0270 overall best weight: 0.4204 ------------------------------------------------------------------------------- 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 203 GLN ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 869 ASN ** 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 = 0.3890 r_free = 0.3890 target = 0.151933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.109521 restraints weight = 16494.516| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.16 r_work: 0.3187 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12055 Z= 0.095 Angle : 0.520 10.234 16429 Z= 0.260 Chirality : 0.044 0.141 1865 Planarity : 0.004 0.050 2127 Dihedral : 3.841 18.008 1673 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.72 % Allowed : 22.36 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.22), residues: 1536 helix: 0.69 (0.34), residues: 256 sheet: -0.23 (0.25), residues: 465 loop : -0.80 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 174 TYR 0.009 0.001 TYR A 911 PHE 0.016 0.001 PHE A 623 TRP 0.018 0.002 TRP A 401 HIS 0.004 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00219 (12055) covalent geometry : angle 0.51982 (16429) hydrogen bonds : bond 0.03256 ( 391) hydrogen bonds : angle 4.47166 ( 1080) ********************** 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 155 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.7848 (mt0) cc_final: 0.7471 (mt0) REVERT: A 157 GLN cc_start: 0.7432 (tt0) cc_final: 0.6982 (tt0) REVERT: A 308 SER cc_start: 0.6977 (OUTLIER) cc_final: 0.6281 (t) REVERT: A 548 ASP cc_start: 0.6816 (m-30) cc_final: 0.6196 (p0) REVERT: A 562 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8007 (pt0) REVERT: B 308 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7484 (mt0) REVERT: B 387 ASP cc_start: 0.8414 (t0) cc_final: 0.8106 (t0) REVERT: B 392 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.8091 (pt) REVERT: C 222 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7672 (mm-30) outliers start: 32 outliers final: 25 residues processed: 147 average time/residue: 0.1125 time to fit residues: 24.3693 Evaluate side-chains 145 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 308 SER 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 812 LEU 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 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 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 75 ASP Chi-restraints excluded: chain C residue 157 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 42 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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** B 383 ASN B 472 GLN ** 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 = 0.3867 r_free = 0.3867 target = 0.149719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.107390 restraints weight = 16689.282| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.15 r_work: 0.3158 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12055 Z= 0.141 Angle : 0.546 10.416 16429 Z= 0.275 Chirality : 0.045 0.149 1865 Planarity : 0.004 0.049 2127 Dihedral : 3.964 17.766 1673 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.64 % Allowed : 22.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.22), residues: 1536 helix: 0.67 (0.34), residues: 256 sheet: -0.26 (0.25), residues: 465 loop : -0.82 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 174 TYR 0.011 0.001 TYR A 717 PHE 0.028 0.002 PHE B 582 TRP 0.016 0.002 TRP B 132 HIS 0.004 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00342 (12055) covalent geometry : angle 0.54624 (16429) hydrogen bonds : bond 0.03625 ( 391) hydrogen bonds : angle 4.53531 ( 1080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2976.55 seconds wall clock time: 51 minutes 45.94 seconds (3105.94 seconds total)