Starting phenix.real_space_refine on Tue Oct 27 21:30:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11yb_76179/10_2026/11yb_76179_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/11yb_76179/10_2026/11yb_76179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11yb_76179/10_2026/11yb_76179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11yb_76179/10_2026/11yb_76179.map" model { file = "/net/cci-nas-00/data/ceres_data/11yb_76179/10_2026/11yb_76179_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11yb_76179/10_2026/11yb_76179_neut.cif" } resolution = 3.4 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= 0.048 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: 7 Type Number sf(0) Gaussians Ca 7 9.91 5 Mg 1 5.21 5 S 101 5.16 5 C 8686 2.51 5 N 2376 2.21 5 O 2718 1.98 5 H 11628 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25517 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 13783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 912, 13783 Classifications: {'peptide': 912} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 58, 'TRANS': 849} Chain breaks: 2 Chain: "B" Number of atoms: 10011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 10011 Classifications: {'peptide': 690} Link IDs: {'PCIS': 3, 'PTRANS': 31, 'TRANS': 655} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "H" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 915 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 112} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 800 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' CA': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.34, per 1000 atoms: 0.17 Number of scatterers: 25517 At special positions: 0 Unit cell: (98.9, 156.52, 130.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 7 19.99 S 101 16.00 Mg 1 11.99 O 2718 8.00 N 2376 7.00 C 8686 6.00 H 11628 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 167 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 545 " distance=2.04 Simple disulfide: pdb=" SG CYS A 602 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 674 " - pdb=" SG CYS A 687 " distance=2.04 Simple disulfide: pdb=" SG CYS A 826 " - pdb=" SG CYS A 890 " distance=2.03 Simple disulfide: pdb=" SG CYS A 880 " - pdb=" SG CYS A 885 " distance=2.04 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 23 " distance=2.03 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 435 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 38 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 406 " - pdb=" SG CYS B 433 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 448 " - pdb=" SG CYS B 460 " distance=2.03 Simple disulfide: pdb=" SG CYS B 462 " - pdb=" SG CYS B 471 " distance=2.03 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 503 " distance=2.03 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 495 " - pdb=" SG CYS B 506 " distance=2.03 Simple disulfide: pdb=" SG CYS B 508 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 523 " - pdb=" SG CYS B 544 " distance=2.03 Simple disulfide: pdb=" SG CYS B 528 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 547 " distance=2.03 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 560 " - pdb=" SG CYS B 583 " distance=2.03 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 581 " distance=2.03 Simple disulfide: pdb=" SG CYS B 575 " - pdb=" SG CYS B 586 " distance=2.03 Simple disulfide: pdb=" SG CYS B 588 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 663 " - pdb=" SG CYS B 687 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 896.8 milliseconds 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3338 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 32 sheets defined 11.7% alpha, 26.4% 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 151 through 158 removed outlier: 3.674A pdb=" N TYR A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 227 through 231 Processing helix chain 'A' and resid 259 through 264 removed outlier: 3.581A pdb=" N THR A 263 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 264 " --> pdb=" O TRP A 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 259 through 264' Processing helix chain 'A' and resid 554 through 558 removed outlier: 3.539A pdb=" N PHE A 558 " --> pdb=" O GLU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.663A pdb=" N GLN A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 40 through 47 Processing helix chain 'B' and resid 76 through 80 removed outlier: 3.845A pdb=" N VAL B 80 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 124 through 129 removed outlier: 3.599A pdb=" N TRP B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 144 removed outlier: 4.295A pdb=" N LYS B 137 " --> pdb=" O ASN B 133 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS B 144 " --> pdb=" O THR B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 199 through 207 removed outlier: 4.230A pdb=" N PHE B 203 " --> pdb=" O GLN B 199 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN B 204 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 232 removed outlier: 4.276A pdb=" N ALA B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 removed outlier: 4.277A pdb=" N ILE B 236 " --> pdb=" O CYS B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 4.076A pdb=" N LEU B 262 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 286 removed outlier: 4.588A pdb=" N THR B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 302 removed outlier: 3.628A pdb=" N LYS B 302 " --> pdb=" O LYS B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 325 removed outlier: 4.538A pdb=" N ASN B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU B 317 " --> pdb=" O ASN B 313 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 352 removed outlier: 3.793A pdb=" N GLY B 349 " --> pdb=" O VAL B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 493 through 498 Processing helix chain 'B' and resid 534 through 539 removed outlier: 3.950A pdb=" N SER B 537 " --> pdb=" O GLU B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 Processing helix chain 'B' and resid 606 through 617 removed outlier: 4.072A pdb=" N PHE B 610 " --> pdb=" O ASP B 606 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL B 615 " --> pdb=" O LYS B 611 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N CYS B 617 " --> pdb=" O GLU B 613 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'L' and resid 48 through 52 removed outlier: 4.137A pdb=" N GLU L 52 " --> pdb=" O SER L 49 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 4.180A pdb=" N SER A 420 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 27 removed outlier: 3.870A pdb=" N SER A 22 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL A 53 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 79 removed outlier: 3.504A pdb=" N GLU A 75 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 97 through 100 Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 175 removed outlier: 3.719A pdb=" N SER A 172 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AA7, first strand: chain 'A' and resid 293 through 296 Processing sheet with id=AA8, first strand: chain 'A' and resid 314 through 315 Processing sheet with id=AA9, first strand: chain 'A' and resid 360 through 362 removed outlier: 3.655A pdb=" N GLN A 405 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 521 through 523 Processing sheet with id=AB2, first strand: chain 'A' and resid 465 through 466 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 612 through 619 removed outlier: 3.820A pdb=" N ASN A 629 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG A 661 " --> pdb=" O LEU A 704 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER A 706 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N TYR A 659 " --> pdb=" O SER A 706 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 674 through 678 removed outlier: 6.708A pdb=" N ALA A 647 " --> pdb=" O LEU A 689 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 749 through 755 removed outlier: 4.152A pdb=" N ASP A 817 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE A 908 " --> pdb=" O ILE A 815 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ILE A 815 " --> pdb=" O PHE A 908 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 758 through 760 removed outlier: 6.986A pdb=" N LEU A 759 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 949 " --> pdb=" O ALA A 928 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 922 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N GLN A 925 " --> pdb=" O PRO A 804 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASN A 795 " --> pdb=" O GLU A 894 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU A 894 " --> pdb=" O ASN A 795 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 758 through 760 removed outlier: 6.986A pdb=" N LEU A 759 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 949 " --> pdb=" O ALA A 928 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 922 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL A 878 " --> pdb=" O GLN A 925 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N HIS A 927 " --> pdb=" O VAL A 878 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AC1, first strand: chain 'B' and resid 63 through 65 removed outlier: 5.214A pdb=" N VAL B 63 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ALA B 89 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE B 88 " --> pdb=" O ILE B 426 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 92 " --> pdb=" O THR B 430 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 84 removed outlier: 3.541A pdb=" N SER B 84 " --> pdb=" O GLN B 103 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 396 " --> pdb=" O THR B 373 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.836A pdb=" N ASP B 113 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL B 247 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TYR B 115 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N THR B 249 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N HIS B 244 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE B 307 " --> pdb=" O HIS B 244 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU B 246 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA B 309 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N PHE B 248 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N THR B 329 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU B 306 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N GLY B 331 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE B 308 " --> pdb=" O GLY B 331 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 118 through 119 removed outlier: 6.544A pdb=" N MET B 118 " --> pdb=" O PHE B 156 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 355 Processing sheet with id=AC6, first strand: chain 'B' and resid 454 through 456 Processing sheet with id=AC7, first strand: chain 'B' and resid 500 through 502 Processing sheet with id=AC8, first strand: chain 'B' and resid 516 through 517 Processing sheet with id=AC9, first strand: chain 'B' and resid 553 through 554 removed outlier: 3.559A pdb=" N CYS B 560 " --> pdb=" O THR B 554 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 580 through 582 Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.412A pdb=" N GLU H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 11 through 12 removed outlier: 3.750A pdb=" N LEU L 103 " --> pdb=" O GLY L 83 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY L 83 " --> pdb=" O LEU L 103 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN L 37 " --> pdb=" O ILE L 84 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 64 through 65 removed outlier: 3.578A pdb=" N SER L 64 " --> pdb=" O ILE L 71 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1041 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: 6.24 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 11628 1.05 - 1.25: 2391 1.25 - 1.46: 5318 1.46 - 1.67: 6344 1.67 - 1.88: 130 Bond restraints: 25811 Sorted by residual: bond pdb=" C CYS B 617 " pdb=" O CYS B 617 " ideal model delta sigma weight residual 1.235 1.515 -0.280 1.26e-02 6.30e+03 4.92e+02 bond pdb=" N CYS B 617 " pdb=" CA CYS B 617 " ideal model delta sigma weight residual 1.457 1.591 -0.134 1.29e-02 6.01e+03 1.07e+02 bond pdb=" CA CYS B 617 " pdb=" CB CYS B 617 " ideal model delta sigma weight residual 1.530 1.682 -0.152 1.69e-02 3.50e+03 8.10e+01 bond pdb=" C HIS B 626 " pdb=" O HIS B 626 " ideal model delta sigma weight residual 1.235 1.318 -0.083 1.26e-02 6.30e+03 4.30e+01 bond pdb=" N ILE L 93 " pdb=" CA ILE L 93 " ideal model delta sigma weight residual 1.461 1.512 -0.051 1.23e-02 6.61e+03 1.71e+01 ... (remaining 25806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.03: 45820 9.03 - 18.05: 5 18.05 - 27.08: 0 27.08 - 36.10: 2 36.10 - 45.13: 2 Bond angle restraints: 45829 Sorted by residual: angle pdb=" N CYS B 617 " pdb=" CA CYS B 617 " pdb=" CB CYS B 617 " ideal model delta sigma weight residual 110.49 138.28 -27.79 1.69e+00 3.50e-01 2.70e+02 angle pdb=" C CYS B 471 " pdb=" N GLU B 472 " pdb=" H GLU B 472 " ideal model delta sigma weight residual 124.56 79.43 45.13 3.00e+00 1.11e-01 2.26e+02 angle pdb=" CA GLU B 472 " pdb=" N GLU B 472 " pdb=" H GLU B 472 " ideal model delta sigma weight residual 114.26 69.16 45.10 3.00e+00 1.11e-01 2.26e+02 angle pdb=" C CYS B 471 " pdb=" N GLU B 472 " pdb=" CA GLU B 472 " ideal model delta sigma weight residual 121.18 148.60 -27.42 1.98e+00 2.55e-01 1.92e+02 angle pdb=" N CYS B 617 " pdb=" CA CYS B 617 " pdb=" C CYS B 617 " ideal model delta sigma weight residual 110.80 94.69 16.11 2.13e+00 2.20e-01 5.72e+01 ... (remaining 45824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 11248 17.93 - 35.85: 951 35.85 - 53.78: 297 53.78 - 71.70: 66 71.70 - 89.63: 10 Dihedral angle restraints: 12572 sinusoidal: 6697 harmonic: 5875 Sorted by residual: dihedral pdb=" CB CYS B 16 " pdb=" SG CYS B 16 " pdb=" SG CYS B 38 " pdb=" CB CYS B 38 " ideal model delta sinusoidal sigma weight residual -86.00 -156.84 70.84 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" N CYS B 617 " pdb=" C CYS B 617 " pdb=" CA CYS B 617 " pdb=" CB CYS B 617 " ideal model delta harmonic sigma weight residual 122.80 142.23 -19.43 0 2.50e+00 1.60e-01 6.04e+01 dihedral pdb=" CB CYS A 490 " pdb=" SG CYS A 490 " pdb=" SG CYS A 545 " pdb=" CB CYS A 545 " ideal model delta sinusoidal sigma weight residual 93.00 35.53 57.47 1 1.00e+01 1.00e-02 4.44e+01 ... (remaining 12569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1733 0.054 - 0.109: 292 0.109 - 0.163: 93 0.163 - 0.217: 4 0.217 - 0.272: 9 Chirality restraints: 2131 Sorted by residual: chirality pdb=" CA GLU H 1 " pdb=" N GLU H 1 " pdb=" C GLU H 1 " pdb=" CB GLU H 1 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA TYR B 669 " pdb=" N TYR B 669 " pdb=" C TYR B 669 " pdb=" CB TYR B 669 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA PHE L 95 " pdb=" N PHE L 95 " pdb=" C PHE L 95 " pdb=" CB PHE L 95 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 2128 not shown) Planarity restraints: 4048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 143 " 0.802 9.50e-02 1.11e+02 2.87e-01 3.12e+02 pdb=" NE ARG B 143 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 143 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG B 143 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 143 " -0.025 2.00e-02 2.50e+03 pdb="HH11 ARG B 143 " -0.197 2.00e-02 2.50e+03 pdb="HH12 ARG B 143 " 0.212 2.00e-02 2.50e+03 pdb="HH21 ARG B 143 " 0.028 2.00e-02 2.50e+03 pdb="HH22 ARG B 143 " -0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 60 " -0.529 9.50e-02 1.11e+02 2.37e-01 3.44e+01 pdb=" NE ARG L 60 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG L 60 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG L 60 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG L 60 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 691 " -0.059 5.00e-02 4.00e+02 8.94e-02 1.28e+01 pdb=" N PRO A 692 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO A 692 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 692 " -0.049 5.00e-02 4.00e+02 ... (remaining 4045 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 583 2.14 - 2.75: 43239 2.75 - 3.37: 65414 3.37 - 3.98: 84774 3.98 - 4.60: 131062 Nonbonded interactions: 325072 Sorted by model distance: nonbonded pdb="HD22 ASN B 215 " pdb="CA CA B 802 " model vdw 1.520 2.040 nonbonded pdb=" H GLU B 472 " pdb=" HA GLU B 472 " model vdw 1.630 1.816 nonbonded pdb="HD21 ASN B 215 " pdb="CA CA B 802 " model vdw 1.723 2.040 nonbonded pdb=" OD1 ASP B 126 " pdb="CA CA B 803 " model vdw 1.739 2.390 nonbonded pdb=" O THR A 250 " pdb="CA CA A1103 " model vdw 1.781 2.390 ... (remaining 325067 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: 6.150 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: 0.070 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 24.590 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 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 : 0.006 0.280 14218 Z= 0.366 Angle : 0.820 27.786 19348 Z= 0.484 Chirality : 0.050 0.272 2131 Planarity : 0.009 0.301 2545 Dihedral : 14.572 89.628 5174 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.99 % Allowed : 7.79 % Favored : 91.22 % Rotamer: Outliers : 3.27 % Allowed : 18.18 % Favored : 78.55 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.19), residues: 1811 helix: -1.25 (0.48), residues: 116 sheet: -0.31 (0.22), residues: 608 loop : -1.91 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 143 TYR 0.014 0.002 TYR A 448 PHE 0.014 0.001 PHE A 19 TRP 0.017 0.001 TRP H 105 HIS 0.003 0.001 HIS B 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.37 (14183) covalent geometry : angle 0.81638 / 0.48 (19278) SS BOND : bond 0.00343 / 0.23 ( 35) SS BOND : angle 1.48520 / 0.98 ( 70) hydrogen bonds : bond 0.14887 / 10.53 ( 408) hydrogen bonds : angle 6.83888 / 4.86 ( 1041) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue ALA 607 is missing expected H atoms. Skipping. Residue THR 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue VAL 615 is missing expected H atoms. Skipping. Residue LYS 618 is missing expected H atoms. Skipping. Residue LYS 619 is missing expected H atoms. Skipping. Residue ALA 624 is missing expected H atoms. Skipping. Residue LEU 625 is missing expected H atoms. Skipping. Residue THR 630 is missing expected H atoms. Skipping. Residue TYR 634 is missing expected H atoms. Skipping. Residue LEU 645 is missing expected H atoms. Skipping. Residue LYS 646 is missing expected H atoms. Skipping. Residue THR 648 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 155 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.8935 (OUTLIER) cc_final: 0.8130 (m-80) outliers start: 50 outliers final: 37 residues processed: 194 average time/residue: 0.2158 time to fit residues: 63.5486 Evaluate side-chains 184 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 675 ASN Chi-restraints excluded: chain A residue 732 ASN Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 583 CYS Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 657 TYR Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 33 TRP Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 95 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 720 GLN ** A 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 GLN ** H 5 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 = 0.4355 r_free = 0.4355 target = 0.185923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.123438 restraints weight = 53848.057| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 3.15 r_work: 0.3429 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.0622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 14218 Z= 0.155 Angle : 0.607 21.135 19348 Z= 0.315 Chirality : 0.044 0.144 2131 Planarity : 0.005 0.089 2545 Dihedral : 7.148 58.750 2029 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.01 % Favored : 91.44 % Rotamer: Outliers : 3.47 % Allowed : 17.53 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.19), residues: 1811 helix: -1.15 (0.45), residues: 122 sheet: -0.34 (0.21), residues: 615 loop : -1.85 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 62 TYR 0.015 0.001 TYR H 95 PHE 0.014 0.001 PHE A 19 TRP 0.014 0.001 TRP H 105 HIS 0.002 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.15 (14183) covalent geometry : angle 0.60191 / 0.31 (19278) SS BOND : bond 0.00312 / 0.21 ( 35) SS BOND : angle 1.38424 / 0.92 ( 70) hydrogen bonds : bond 0.04155 / 2.78 ( 408) hydrogen bonds : angle 5.77111 / 4.02 ( 1041) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue ALA 607 is missing expected H atoms. Skipping. Residue THR 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue VAL 615 is missing expected H atoms. Skipping. Residue LYS 618 is missing expected H atoms. Skipping. Residue LYS 619 is missing expected H atoms. Skipping. Residue ALA 624 is missing expected H atoms. Skipping. Residue LEU 625 is missing expected H atoms. Skipping. Residue THR 630 is missing expected H atoms. Skipping. Residue TYR 634 is missing expected H atoms. Skipping. Residue LEU 645 is missing expected H atoms. Skipping. Residue LYS 646 is missing expected H atoms. Skipping. Residue THR 648 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 149 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: B 42 GLU cc_start: 0.8388 (mp0) cc_final: 0.8032 (mp0) REVERT: B 657 TYR cc_start: 0.5811 (OUTLIER) cc_final: 0.5060 (p90) REVERT: H 20 MET cc_start: 0.7196 (mtp) cc_final: 0.6892 (mtp) REVERT: H 78 THR cc_start: 0.7903 (p) cc_final: 0.7696 (p) REVERT: L 82 GLU cc_start: 0.7649 (pp20) cc_final: 0.7194 (pp20) outliers start: 53 outliers final: 37 residues processed: 190 average time/residue: 0.2118 time to fit residues: 61.9400 Evaluate side-chains 181 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 732 ASN Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 583 CYS Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 657 TYR Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 33 TRP Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 26 GLN Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 84 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: [136, 157, 43, 172, 133, 177, 153, 67, 137, 106, 55] chunk 136 optimal weight: 0.0000 chunk 157 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 172 optimal weight: 7.9990 chunk 133 optimal weight: 0.6980 chunk 177 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 GLN ** H 5 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 = 0.4338 r_free = 0.4338 target = 0.185652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.118539 restraints weight = 53263.137| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.75 r_work: 0.3424 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14218 Z= 0.172 Angle : 0.600 19.961 19348 Z= 0.312 Chirality : 0.044 0.142 2131 Planarity : 0.005 0.089 2545 Dihedral : 6.307 58.760 2000 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.95 % Favored : 91.44 % Rotamer: Outliers : 3.73 % Allowed : 18.18 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.19), residues: 1811 helix: -1.03 (0.45), residues: 125 sheet: -0.36 (0.21), residues: 615 loop : -1.87 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 62 TYR 0.017 0.002 TYR H 95 PHE 0.017 0.002 PHE A 19 TRP 0.017 0.001 TRP H 105 HIS 0.003 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 (14183) covalent geometry : angle 0.59447 / 0.31 (19278) SS BOND : bond 0.00353 / 0.23 ( 35) SS BOND : angle 1.50723 / 1.08 ( 70) hydrogen bonds : bond 0.03890 / 2.64 ( 408) hydrogen bonds : angle 5.55766 / 3.85 ( 1041) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue ALA 607 is missing expected H atoms. Skipping. Residue THR 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue VAL 615 is missing expected H atoms. Skipping. Residue LYS 618 is missing expected H atoms. Skipping. Residue LYS 619 is missing expected H atoms. Skipping. Residue ALA 624 is missing expected H atoms. Skipping. Residue LEU 625 is missing expected H atoms. Skipping. Residue THR 630 is missing expected H atoms. Skipping. Residue TYR 634 is missing expected H atoms. Skipping. Residue LEU 645 is missing expected H atoms. Skipping. Residue LYS 646 is missing expected H atoms. Skipping. Residue THR 648 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 152 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.8014 (m-80) REVERT: A 549 MET cc_start: 0.6033 (tpp) cc_final: 0.5468 (tpp) REVERT: B 178 TYR cc_start: 0.7960 (t80) cc_final: 0.7700 (t80) REVERT: B 657 TYR cc_start: 0.5947 (OUTLIER) cc_final: 0.5284 (p90) outliers start: 57 outliers final: 42 residues processed: 196 average time/residue: 0.2094 time to fit residues: 61.9340 Evaluate side-chains 191 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 732 ASN Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 583 CYS Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 657 TYR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 33 TRP Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 26 GLN Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 84 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: [150, 24, 80, 143, 6, 88, 2, 94, 139, 15, 50] chunk 150 optimal weight: 0.8980 chunk 24 optimal weight: 0.0040 chunk 80 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 overall best weight: 1.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 691 ASN ** A 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.183557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.117285 restraints weight = 53227.373| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.11 r_work: 0.3369 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 14218 Z= 0.213 Angle : 0.631 20.230 19348 Z= 0.329 Chirality : 0.045 0.154 2131 Planarity : 0.005 0.091 2545 Dihedral : 6.246 58.374 1995 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.39 % Favored : 90.01 % Rotamer: Outliers : 4.77 % Allowed : 17.33 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.19), residues: 1811 helix: -1.20 (0.43), residues: 125 sheet: -0.48 (0.22), residues: 612 loop : -1.92 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 32 TYR 0.019 0.002 TYR H 95 PHE 0.020 0.002 PHE A 19 TRP 0.019 0.001 TRP H 105 HIS 0.004 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.21 (14183) covalent geometry : angle 0.62530 / 0.33 (19278) SS BOND : bond 0.00323 / 0.21 ( 35) SS BOND : angle 1.58749 / 1.16 ( 70) hydrogen bonds : bond 0.03874 / 2.60 ( 408) hydrogen bonds : angle 5.55452 / 3.84 ( 1041) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue ALA 607 is missing expected H atoms. Skipping. Residue THR 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue VAL 615 is missing expected H atoms. Skipping. Residue LYS 618 is missing expected H atoms. Skipping. Residue LYS 619 is missing expected H atoms. Skipping. Residue ALA 624 is missing expected H atoms. Skipping. Residue LEU 625 is missing expected H atoms. Skipping. Residue THR 630 is missing expected H atoms. Skipping. Residue TYR 634 is missing expected H atoms. Skipping. Residue LEU 645 is missing expected H atoms. Skipping. Residue LYS 646 is missing expected H atoms. Skipping. Residue THR 648 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 147 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.8991 (OUTLIER) cc_final: 0.7933 (m-80) REVERT: A 497 ASN cc_start: 0.6651 (t0) cc_final: 0.6437 (t0) REVERT: A 549 MET cc_start: 0.6208 (tpp) cc_final: 0.5661 (tpp) REVERT: A 902 MET cc_start: 0.7424 (ttp) cc_final: 0.7022 (ttm) REVERT: B 42 GLU cc_start: 0.8496 (mp0) cc_final: 0.8169 (mp0) REVERT: B 178 TYR cc_start: 0.8091 (t80) cc_final: 0.7869 (t80) REVERT: B 341 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6226 (tp) REVERT: B 342 GLN cc_start: 0.6037 (tm-30) cc_final: 0.5830 (tm-30) REVERT: B 657 TYR cc_start: 0.6229 (OUTLIER) cc_final: 0.5645 (p90) REVERT: L 20 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8170 (mt) outliers start: 73 outliers final: 53 residues processed: 210 average time/residue: 0.2129 time to fit residues: 67.9300 Evaluate side-chains 197 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 140 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 732 ASN Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 583 CYS Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 657 TYR Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 33 TRP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 26 GLN Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 95 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: [47, 71, 1, 105, 81, 119, 170, 118, 58, 94, 72] chunk 47 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.184472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.117888 restraints weight = 52956.733| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.76 r_work: 0.3416 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14218 Z= 0.155 Angle : 0.605 20.216 19348 Z= 0.313 Chirality : 0.044 0.297 2131 Planarity : 0.005 0.092 2545 Dihedral : 6.082 57.714 1992 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.17 % Favored : 91.28 % Rotamer: Outliers : 3.92 % Allowed : 18.44 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.19), residues: 1811 helix: -0.92 (0.45), residues: 125 sheet: -0.60 (0.21), residues: 634 loop : -1.88 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.015 0.001 TYR H 95 PHE 0.015 0.001 PHE A 19 TRP 0.017 0.001 TRP H 105 HIS 0.003 0.001 HIS A 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.15 (14183) covalent geometry : angle 0.59876 / 0.31 (19278) SS BOND : bond 0.00665 / 0.50 ( 35) SS BOND : angle 1.52847 / 1.04 ( 70) hydrogen bonds : bond 0.03530 / 2.37 ( 408) hydrogen bonds : angle 5.42090 / 3.74 ( 1041) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue ALA 607 is missing expected H atoms. Skipping. Residue THR 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue VAL 615 is missing expected H atoms. Skipping. Residue LYS 618 is missing expected H atoms. Skipping. Residue LYS 619 is missing expected H atoms. Skipping. Residue ALA 624 is missing expected H atoms. Skipping. Residue LEU 625 is missing expected H atoms. Skipping. Residue THR 630 is missing expected H atoms. Skipping. Residue TYR 634 is missing expected H atoms. Skipping. Residue LEU 645 is missing expected H atoms. Skipping. Residue LYS 646 is missing expected H atoms. Skipping. Residue THR 648 is missing expected H atoms. Skipping. Evaluate side-chains 204 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 144 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.7911 (m-80) REVERT: A 497 ASN cc_start: 0.6655 (t0) cc_final: 0.6431 (t0) REVERT: A 902 MET cc_start: 0.7532 (ttp) cc_final: 0.7119 (ttm) REVERT: B 28 ASP cc_start: 0.6828 (t0) cc_final: 0.6547 (t0) REVERT: B 178 TYR cc_start: 0.8021 (t80) cc_final: 0.7812 (t80) REVERT: B 217 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7417 (t0) REVERT: B 341 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6155 (tp) REVERT: B 657 TYR cc_start: 0.6149 (OUTLIER) cc_final: 0.5462 (p90) outliers start: 60 outliers final: 48 residues processed: 191 average time/residue: 0.2099 time to fit residues: 61.7278 Evaluate side-chains 190 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 138 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 732 ASN Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 583 CYS Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 657 TYR Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 33 TRP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: [20, 173, 152, 169, 56, 146, 180, 59, 34, 119, 127] chunk 20 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 chunk 152 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 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 = 0.4311 r_free = 0.4311 target = 0.183247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.123396 restraints weight = 53254.847| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.13 r_work: 0.3383 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14218 Z= 0.192 Angle : 0.622 20.298 19348 Z= 0.322 Chirality : 0.045 0.315 2131 Planarity : 0.005 0.093 2545 Dihedral : 6.138 58.060 1990 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.55 % Allowed : 9.50 % Favored : 89.95 % Rotamer: Outliers : 4.51 % Allowed : 18.31 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.19), residues: 1811 helix: -0.92 (0.44), residues: 125 sheet: -0.63 (0.21), residues: 627 loop : -1.91 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.017 0.002 TYR H 95 PHE 0.018 0.002 PHE A 19 TRP 0.017 0.001 TRP H 105 HIS 0.003 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 (14183) covalent geometry : angle 0.61723 / 0.32 (19278) SS BOND : bond 0.00647 / 0.48 ( 35) SS BOND : angle 1.42383 / 0.98 ( 70) hydrogen bonds : bond 0.03702 / 2.48 ( 408) hydrogen bonds : angle 5.46098 / 3.78 ( 1041) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue ALA 607 is missing expected H atoms. Skipping. Residue THR 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue VAL 615 is missing expected H atoms. Skipping. Residue LYS 618 is missing expected H atoms. Skipping. Residue LYS 619 is missing expected H atoms. Skipping. Residue ALA 624 is missing expected H atoms. Skipping. Residue LEU 625 is missing expected H atoms. Skipping. Residue THR 630 is missing expected H atoms. Skipping. Residue TYR 634 is missing expected H atoms. Skipping. Residue LEU 645 is missing expected H atoms. Skipping. Residue LYS 646 is missing expected H atoms. Skipping. Residue THR 648 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 145 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.8975 (OUTLIER) cc_final: 0.7853 (m-80) REVERT: A 497 ASN cc_start: 0.6701 (t0) cc_final: 0.6469 (t0) REVERT: A 549 MET cc_start: 0.6592 (mmm) cc_final: 0.6181 (tpp) REVERT: A 902 MET cc_start: 0.7534 (ttp) cc_final: 0.7121 (ttm) REVERT: B 28 ASP cc_start: 0.6761 (t0) cc_final: 0.6468 (t0) REVERT: B 106 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.6890 (mp10) REVERT: B 217 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7455 (t0) REVERT: B 341 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6189 (tp) REVERT: B 647 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.7028 (t0) REVERT: B 657 TYR cc_start: 0.6355 (OUTLIER) cc_final: 0.5605 (p90) REVERT: H 74 LYS cc_start: 0.4023 (OUTLIER) cc_final: 0.2879 (ptpt) outliers start: 69 outliers final: 53 residues processed: 201 average time/residue: 0.2093 time to fit residues: 64.4878 Evaluate side-chains 200 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 140 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 545 CYS Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 732 ASN Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 583 CYS Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 657 TYR Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 33 TRP Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 26 GLN Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 62 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: [159, 67, 127, 174, 151, 154, 147, 80, 161, 1, 178] chunk 159 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 127 optimal weight: 0.0970 chunk 174 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 161 optimal weight: 0.0070 chunk 1 optimal weight: 0.9980 chunk 178 optimal weight: 7.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 GLN ** H 5 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 = 0.4338 r_free = 0.4338 target = 0.185981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.119670 restraints weight = 52590.549| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.74 r_work: 0.3438 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 14218 Z= 0.103 Angle : 0.578 20.191 19348 Z= 0.296 Chirality : 0.043 0.296 2131 Planarity : 0.004 0.092 2545 Dihedral : 5.856 58.247 1990 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.63 % Favored : 92.93 % Rotamer: Outliers : 3.47 % Allowed : 18.97 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.20), residues: 1811 helix: -0.60 (0.46), residues: 125 sheet: -0.46 (0.21), residues: 629 loop : -1.77 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.014 0.001 TYR L 29 PHE 0.010 0.001 PHE B 248 TRP 0.013 0.001 TRP H 105 HIS 0.006 0.001 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.10 (14183) covalent geometry : angle 0.57309 / 0.29 (19278) SS BOND : bond 0.00620 / 0.47 ( 35) SS BOND : angle 1.37256 / 0.95 ( 70) hydrogen bonds : bond 0.03089 / 2.08 ( 408) hydrogen bonds : angle 5.21986 / 3.59 ( 1041) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue ALA 607 is missing expected H atoms. Skipping. Residue THR 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue VAL 615 is missing expected H atoms. Skipping. Residue LYS 618 is missing expected H atoms. Skipping. Residue LYS 619 is missing expected H atoms. Skipping. Residue ALA 624 is missing expected H atoms. Skipping. Residue LEU 625 is missing expected H atoms. Skipping. Residue THR 630 is missing expected H atoms. Skipping. Residue TYR 634 is missing expected H atoms. Skipping. Residue LEU 645 is missing expected H atoms. Skipping. Residue LYS 646 is missing expected H atoms. Skipping. Residue THR 648 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 146 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.8876 (OUTLIER) cc_final: 0.7783 (m-80) REVERT: A 497 ASN cc_start: 0.6671 (t0) cc_final: 0.6433 (t0) REVERT: A 549 MET cc_start: 0.6564 (mmm) cc_final: 0.6120 (tpp) REVERT: A 899 GLN cc_start: 0.6434 (tt0) cc_final: 0.5924 (mm-40) REVERT: A 902 MET cc_start: 0.7516 (ttp) cc_final: 0.7093 (ttm) REVERT: B 28 ASP cc_start: 0.6727 (t0) cc_final: 0.6430 (t0) REVERT: B 42 GLU cc_start: 0.8118 (mp0) cc_final: 0.7898 (mp0) REVERT: B 178 TYR cc_start: 0.8002 (t80) cc_final: 0.7754 (t80) REVERT: B 341 LEU cc_start: 0.6289 (OUTLIER) cc_final: 0.6012 (tp) REVERT: B 365 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6541 (pt0) REVERT: B 647 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6816 (t0) REVERT: B 657 TYR cc_start: 0.6092 (OUTLIER) cc_final: 0.5314 (p90) REVERT: H 59 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7327 (tp30) outliers start: 53 outliers final: 45 residues processed: 186 average time/residue: 0.2218 time to fit residues: 63.2061 Evaluate side-chains 189 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 139 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 545 CYS Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 732 ASN Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 583 CYS Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 657 TYR Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 33 TRP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 42 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: [137, 8, 162, 130, 100, 48, 102, 38, 97, 74, 178] chunk 137 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 178 optimal weight: 0.0470 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 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 = 0.4329 r_free = 0.4329 target = 0.185089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.118124 restraints weight = 53280.087| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.81 r_work: 0.3419 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14218 Z= 0.139 Angle : 0.589 20.232 19348 Z= 0.302 Chirality : 0.044 0.295 2131 Planarity : 0.004 0.093 2545 Dihedral : 5.836 59.008 1990 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.90 % Favored : 91.66 % Rotamer: Outliers : 3.40 % Allowed : 19.16 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.20), residues: 1811 helix: -0.47 (0.46), residues: 125 sheet: -0.47 (0.21), residues: 625 loop : -1.80 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.015 0.001 TYR B 318 PHE 0.013 0.001 PHE A 19 TRP 0.015 0.001 TRP H 105 HIS 0.007 0.001 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (14183) covalent geometry : angle 0.58405 / 0.30 (19278) SS BOND : bond 0.00623 / 0.47 ( 35) SS BOND : angle 1.38226 / 0.94 ( 70) hydrogen bonds : bond 0.03237 / 2.16 ( 408) hydrogen bonds : angle 5.20009 / 3.58 ( 1041) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue ALA 607 is missing expected H atoms. Skipping. Residue THR 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue VAL 615 is missing expected H atoms. Skipping. Residue LYS 618 is missing expected H atoms. Skipping. Residue LYS 619 is missing expected H atoms. Skipping. Residue ALA 624 is missing expected H atoms. Skipping. Residue LEU 625 is missing expected H atoms. Skipping. Residue THR 630 is missing expected H atoms. Skipping. Residue TYR 634 is missing expected H atoms. Skipping. Residue LEU 645 is missing expected H atoms. Skipping. Residue LYS 646 is missing expected H atoms. Skipping. Residue THR 648 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 141 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.8923 (OUTLIER) cc_final: 0.7888 (m-80) REVERT: A 489 MET cc_start: 0.8169 (pmm) cc_final: 0.7818 (pmm) REVERT: A 497 ASN cc_start: 0.6712 (t0) cc_final: 0.6484 (t0) REVERT: A 549 MET cc_start: 0.6673 (mmm) cc_final: 0.6134 (tpp) REVERT: A 703 MET cc_start: 0.7907 (ttp) cc_final: 0.7689 (ttp) REVERT: A 899 GLN cc_start: 0.6391 (tt0) cc_final: 0.5875 (mm-40) REVERT: A 902 MET cc_start: 0.7524 (ttp) cc_final: 0.7102 (ttm) REVERT: B 28 ASP cc_start: 0.6826 (t0) cc_final: 0.6521 (t0) REVERT: B 42 GLU cc_start: 0.8128 (mp0) cc_final: 0.7904 (mp0) REVERT: B 178 TYR cc_start: 0.8032 (t80) cc_final: 0.7779 (t80) REVERT: B 217 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7388 (t0) REVERT: B 341 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.6054 (tp) REVERT: B 365 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6608 (pt0) REVERT: B 647 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.6994 (t0) REVERT: B 657 TYR cc_start: 0.6275 (OUTLIER) cc_final: 0.5556 (p90) REVERT: H 59 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7380 (tp30) outliers start: 52 outliers final: 42 residues processed: 181 average time/residue: 0.2140 time to fit residues: 59.8538 Evaluate side-chains 188 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 140 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 545 CYS Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 732 ASN Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 583 CYS Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 657 TYR Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 33 TRP Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 42 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: [56, 4, 98, 103, 23, 139, 94, 141, 32, 144, 43] chunk 56 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 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 = 0.4312 r_free = 0.4312 target = 0.183328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.116699 restraints weight = 53178.913| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.81 r_work: 0.3387 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14218 Z= 0.191 Angle : 0.624 20.265 19348 Z= 0.322 Chirality : 0.045 0.292 2131 Planarity : 0.005 0.094 2545 Dihedral : 5.866 57.891 1988 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.61 % Favored : 89.95 % Rotamer: Outliers : 3.86 % Allowed : 18.90 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.20), residues: 1811 helix: -0.62 (0.46), residues: 125 sheet: -0.60 (0.21), residues: 627 loop : -1.85 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 279 TYR 0.018 0.002 TYR B 318 PHE 0.018 0.002 PHE A 19 TRP 0.019 0.001 TRP H 105 HIS 0.007 0.001 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 (14183) covalent geometry : angle 0.61922 / 0.32 (19278) SS BOND : bond 0.00638 / 0.48 ( 35) SS BOND : angle 1.42814 / 0.97 ( 70) hydrogen bonds : bond 0.03638 / 2.43 ( 408) hydrogen bonds : angle 5.34443 / 3.68 ( 1041) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue ALA 607 is missing expected H atoms. Skipping. Residue THR 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue VAL 615 is missing expected H atoms. Skipping. Residue LYS 618 is missing expected H atoms. Skipping. Residue LYS 619 is missing expected H atoms. Skipping. Residue ALA 624 is missing expected H atoms. Skipping. Residue LEU 625 is missing expected H atoms. Skipping. Residue THR 630 is missing expected H atoms. Skipping. Residue TYR 634 is missing expected H atoms. Skipping. Residue LEU 645 is missing expected H atoms. Skipping. Residue LYS 646 is missing expected H atoms. Skipping. Residue THR 648 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 138 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.8974 (OUTLIER) cc_final: 0.7950 (m-80) REVERT: A 489 MET cc_start: 0.8212 (pmm) cc_final: 0.7857 (pmm) REVERT: A 497 ASN cc_start: 0.6808 (t0) cc_final: 0.6586 (t0) REVERT: A 549 MET cc_start: 0.6844 (mmm) cc_final: 0.6136 (tpp) REVERT: A 703 MET cc_start: 0.7841 (ttp) cc_final: 0.7609 (ttp) REVERT: A 899 GLN cc_start: 0.6675 (tt0) cc_final: 0.6015 (mm-40) REVERT: A 902 MET cc_start: 0.7519 (ttp) cc_final: 0.7100 (ttm) REVERT: B 28 ASP cc_start: 0.6676 (t0) cc_final: 0.6470 (t0) REVERT: B 42 GLU cc_start: 0.8152 (mp0) cc_final: 0.7913 (mp0) REVERT: B 106 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.6827 (mp10) REVERT: B 341 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.6174 (tp) REVERT: B 365 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6742 (pt0) REVERT: B 647 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.7021 (t0) REVERT: B 657 TYR cc_start: 0.6544 (OUTLIER) cc_final: 0.5762 (p90) REVERT: H 78 THR cc_start: 0.8056 (p) cc_final: 0.7811 (p) outliers start: 59 outliers final: 45 residues processed: 186 average time/residue: 0.2119 time to fit residues: 60.1515 Evaluate side-chains 188 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 137 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 545 CYS Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 732 ASN Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 583 CYS Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 657 TYR Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 33 TRP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: [77, 145, 114, 42, 39, 31, 175, 136, 29, 96, 2] chunk 77 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 chunk 2 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 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 = 0.4337 r_free = 0.4337 target = 0.185929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.124433 restraints weight = 53273.069| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 3.36 r_work: 0.3399 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14218 Z= 0.105 Angle : 0.580 20.256 19348 Z= 0.296 Chirality : 0.044 0.283 2131 Planarity : 0.004 0.093 2545 Dihedral : 5.589 56.902 1987 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.23 % Favored : 92.32 % Rotamer: Outliers : 2.88 % Allowed : 19.82 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.20), residues: 1811 helix: -0.34 (0.47), residues: 127 sheet: -0.41 (0.21), residues: 619 loop : -1.75 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 87 TYR 0.013 0.001 TYR B 318 PHE 0.011 0.001 PHE B 248 TRP 0.012 0.001 TRP H 105 HIS 0.007 0.001 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.10 (14183) covalent geometry : angle 0.57571 / 0.29 (19278) SS BOND : bond 0.00615 / 0.46 ( 35) SS BOND : angle 1.33118 / 0.89 ( 70) hydrogen bonds : bond 0.03049 / 2.05 ( 408) hydrogen bonds : angle 5.13645 / 3.52 ( 1041) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3622 Ramachandran restraints generated. 1811 Oldfield, 0 Emsley, 1811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue ALA 607 is missing expected H atoms. Skipping. Residue THR 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue VAL 615 is missing expected H atoms. Skipping. Residue LYS 618 is missing expected H atoms. Skipping. Residue LYS 619 is missing expected H atoms. Skipping. Residue ALA 624 is missing expected H atoms. Skipping. Residue LEU 625 is missing expected H atoms. Skipping. Residue THR 630 is missing expected H atoms. Skipping. Residue TYR 634 is missing expected H atoms. Skipping. Residue LEU 645 is missing expected H atoms. Skipping. Residue LYS 646 is missing expected H atoms. Skipping. Residue THR 648 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 142 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.8906 (OUTLIER) cc_final: 0.7820 (m-80) REVERT: A 489 MET cc_start: 0.8306 (pmm) cc_final: 0.7937 (pmm) REVERT: A 549 MET cc_start: 0.6952 (mmm) cc_final: 0.6187 (tpp) REVERT: A 703 MET cc_start: 0.7856 (ttp) cc_final: 0.7628 (ttp) REVERT: A 899 GLN cc_start: 0.6703 (tt0) cc_final: 0.6055 (mm-40) REVERT: A 902 MET cc_start: 0.7570 (ttp) cc_final: 0.7046 (ttm) REVERT: B 28 ASP cc_start: 0.6745 (t0) cc_final: 0.6542 (t0) REVERT: B 42 GLU cc_start: 0.8149 (mp0) cc_final: 0.7948 (mp0) REVERT: B 178 TYR cc_start: 0.8019 (t80) cc_final: 0.7745 (t80) REVERT: B 318 TYR cc_start: 0.9115 (m-80) cc_final: 0.8911 (m-80) REVERT: B 341 LEU cc_start: 0.6312 (OUTLIER) cc_final: 0.6051 (tp) REVERT: B 365 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6681 (pt0) REVERT: B 647 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.6880 (t0) REVERT: B 657 TYR cc_start: 0.6332 (OUTLIER) cc_final: 0.5515 (p90) REVERT: H 34 MET cc_start: 0.6715 (mmt) cc_final: 0.6341 (mmm) REVERT: H 59 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7368 (tp30) outliers start: 44 outliers final: 37 residues processed: 175 average time/residue: 0.2238 time to fit residues: 60.1234 Evaluate side-chains 180 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 138 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 545 CYS Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 732 ASN Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 583 CYS Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 657 TYR Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 33 TRP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 42 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: [28, 75, 48, 140, 87, 175, 90, 137, 45, 165, 172] chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 48 optimal weight: 0.2980 chunk 140 optimal weight: 9.9990 chunk 87 optimal weight: 0.4980 chunk 175 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 172 optimal weight: 8.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 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 = 0.4322 r_free = 0.4322 target = 0.184472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.117102 restraints weight = 53727.384| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.84 r_work: 0.3398 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14218 Z= 0.152 Angle : 0.597 20.287 19348 Z= 0.306 Chirality : 0.044 0.285 2131 Planarity : 0.005 0.093 2545 Dihedral : 5.523 57.566 1984 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.61 % Favored : 90.94 % Rotamer: Outliers : 3.01 % Allowed : 19.69 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.20), residues: 1811 helix: -0.34 (0.47), residues: 127 sheet: -0.48 (0.21), residues: 625 loop : -1.76 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 32 TYR 0.015 0.001 TYR B 318 PHE 0.020 0.001 PHE B 223 TRP 0.017 0.001 TRP H 105 HIS 0.006 0.001 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 (14183) covalent geometry : angle 0.59260 / 0.30 (19278) SS BOND : bond 0.00625 / 0.47 ( 35) SS BOND : angle 1.37277 / 0.92 ( 70) hydrogen bonds : bond 0.03315 / 2.22 ( 408) hydrogen bonds : angle 5.17279 / 3.55 ( 1041) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7608.51 seconds wall clock time: 129 minutes 25.83 seconds (7765.83 seconds total)