Starting phenix.real_space_refine on Fri Jan 16 03:46:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ufr_26478/01_2026/7ufr_26478.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ufr_26478/01_2026/7ufr_26478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ufr_26478/01_2026/7ufr_26478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ufr_26478/01_2026/7ufr_26478.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ufr_26478/01_2026/7ufr_26478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ufr_26478/01_2026/7ufr_26478.map" } resolution = 2.7 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= -0.001 sd= 1.374 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 108 5.16 5 C 20552 2.51 5 N 5656 2.21 5 O 6232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32552 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8137 Classifications: {'peptide': 1038} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 57, 'TRANS': 980} Chain: "B" Number of atoms: 8137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8137 Classifications: {'peptide': 1038} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 57, 'TRANS': 980} Chain: "C" Number of atoms: 8137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8137 Classifications: {'peptide': 1038} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 57, 'TRANS': 980} Chain: "D" Number of atoms: 8137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8137 Classifications: {'peptide': 1038} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 57, 'TRANS': 980} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.92, per 1000 atoms: 0.21 Number of scatterers: 32552 At special positions: 0 Unit cell: (98.49, 144.05, 169.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 108 16.00 O 6232 8.00 N 5656 7.00 C 20552 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 597 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 275 " pdb=" ZN B1101 " pdb="ZN ZN B1101 " - pdb=" NE2 HIS B 597 " pdb="ZN ZN B1101 " - pdb=" NE2 HIS B 275 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 597 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 275 " pdb=" ZN D1101 " pdb="ZN ZN D1101 " - pdb=" NE2 HIS D 597 " pdb="ZN ZN D1101 " - pdb=" NE2 HIS D 275 " 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7680 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 44 sheets defined 30.7% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 4 through 20 removed outlier: 3.907A pdb=" N VAL A 20 " --> pdb=" O VAL A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 24 Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 197 through 215 removed outlier: 3.757A pdb=" N GLU A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 238 removed outlier: 3.547A pdb=" N TRP A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 258 removed outlier: 4.016A pdb=" N ALA A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLY A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 305 removed outlier: 3.893A pdb=" N ARG A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 325 Processing helix chain 'A' and resid 325 through 338 removed outlier: 3.609A pdb=" N GLU A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 376 Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 410 through 415 removed outlier: 3.630A pdb=" N SER A 413 " --> pdb=" O GLN A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 461 Processing helix chain 'A' and resid 484 through 494 removed outlier: 3.934A pdb=" N ARG A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 524 Processing helix chain 'A' and resid 539 through 544 removed outlier: 3.798A pdb=" N LEU A 543 " --> pdb=" O ARG A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 572 removed outlier: 4.000A pdb=" N LYS A 550 " --> pdb=" O GLN A 546 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR A 562 " --> pdb=" O SER A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 595 removed outlier: 3.513A pdb=" N LEU A 584 " --> pdb=" O PRO A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 638 Processing helix chain 'A' and resid 738 through 742 Processing helix chain 'A' and resid 833 through 839 removed outlier: 3.865A pdb=" N LYS A 839 " --> pdb=" O SER A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 930 Processing helix chain 'A' and resid 987 through 990 Processing helix chain 'B' and resid 4 through 20 removed outlier: 3.908A pdb=" N VAL B 20 " --> pdb=" O VAL B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 24 Processing helix chain 'B' and resid 44 through 55 Processing helix chain 'B' and resid 197 through 215 removed outlier: 3.757A pdb=" N GLU B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 238 removed outlier: 3.546A pdb=" N TRP B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 258 removed outlier: 4.016A pdb=" N ALA B 248 " --> pdb=" O GLU B 244 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLY B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 305 removed outlier: 3.894A pdb=" N ARG B 289 " --> pdb=" O ARG B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 325 Processing helix chain 'B' and resid 325 through 338 removed outlier: 3.609A pdb=" N GLU B 338 " --> pdb=" O ARG B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 376 Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 410 through 415 removed outlier: 3.635A pdb=" N SER B 413 " --> pdb=" O GLN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 461 Processing helix chain 'B' and resid 484 through 494 removed outlier: 3.934A pdb=" N ARG B 493 " --> pdb=" O GLU B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 524 Processing helix chain 'B' and resid 539 through 544 removed outlier: 3.798A pdb=" N LEU B 543 " --> pdb=" O ARG B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 572 removed outlier: 4.000A pdb=" N LYS B 550 " --> pdb=" O GLN B 546 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR B 562 " --> pdb=" O SER B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 595 Processing helix chain 'B' and resid 605 through 638 Processing helix chain 'B' and resid 833 through 839 removed outlier: 3.865A pdb=" N LYS B 839 " --> pdb=" O SER B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 930 Processing helix chain 'B' and resid 987 through 990 Processing helix chain 'C' and resid 4 through 20 removed outlier: 3.909A pdb=" N VAL C 20 " --> pdb=" O VAL C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 44 through 55 Processing helix chain 'C' and resid 197 through 215 removed outlier: 3.757A pdb=" N GLU C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 238 removed outlier: 3.547A pdb=" N TRP C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 258 removed outlier: 4.026A pdb=" N ALA C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLY C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL C 256 " --> pdb=" O VAL C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 305 removed outlier: 3.893A pdb=" N ARG C 289 " --> pdb=" O ARG C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 325 Processing helix chain 'C' and resid 325 through 338 removed outlier: 3.609A pdb=" N GLU C 338 " --> pdb=" O ARG C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 376 Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 410 through 415 removed outlier: 3.635A pdb=" N SER C 413 " --> pdb=" O GLN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 461 Processing helix chain 'C' and resid 484 through 494 removed outlier: 3.934A pdb=" N ARG C 493 " --> pdb=" O GLU C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 524 Processing helix chain 'C' and resid 539 through 544 removed outlier: 3.798A pdb=" N LEU C 543 " --> pdb=" O ARG C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 572 removed outlier: 4.001A pdb=" N LYS C 550 " --> pdb=" O GLN C 546 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR C 562 " --> pdb=" O SER C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 595 Processing helix chain 'C' and resid 605 through 638 Processing helix chain 'C' and resid 833 through 839 removed outlier: 3.862A pdb=" N LYS C 839 " --> pdb=" O SER C 835 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 930 Processing helix chain 'C' and resid 987 through 990 Processing helix chain 'D' and resid 4 through 20 removed outlier: 3.908A pdb=" N VAL D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 24 Processing helix chain 'D' and resid 44 through 55 Processing helix chain 'D' and resid 197 through 215 removed outlier: 3.755A pdb=" N GLU D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 238 removed outlier: 3.547A pdb=" N TRP D 225 " --> pdb=" O SER D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 258 removed outlier: 4.016A pdb=" N ALA D 248 " --> pdb=" O GLU D 244 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 252 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLY D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL D 256 " --> pdb=" O VAL D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 305 removed outlier: 3.894A pdb=" N ARG D 289 " --> pdb=" O ARG D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 325 Processing helix chain 'D' and resid 325 through 338 removed outlier: 3.609A pdb=" N GLU D 338 " --> pdb=" O ARG D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 376 Processing helix chain 'D' and resid 394 through 403 Processing helix chain 'D' and resid 410 through 415 removed outlier: 3.635A pdb=" N SER D 413 " --> pdb=" O GLN D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 461 Processing helix chain 'D' and resid 484 through 494 removed outlier: 3.933A pdb=" N ARG D 493 " --> pdb=" O GLU D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 524 Processing helix chain 'D' and resid 539 through 544 removed outlier: 3.798A pdb=" N LEU D 543 " --> pdb=" O ARG D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 572 removed outlier: 4.000A pdb=" N LYS D 550 " --> pdb=" O GLN D 546 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR D 562 " --> pdb=" O SER D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 595 Processing helix chain 'D' and resid 605 through 638 Processing helix chain 'D' and resid 833 through 839 removed outlier: 3.865A pdb=" N LYS D 839 " --> pdb=" O SER D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 917 through 930 Processing helix chain 'D' and resid 987 through 990 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 6.621A pdb=" N LEU A 193 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLN A 30 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ALA A 191 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER A 190 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 62 removed outlier: 4.402A pdb=" N VAL A 33 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 469 through 474 removed outlier: 6.439A pdb=" N ASN A 267 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU A 472 " --> pdb=" O ASN A 267 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N SER A 269 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N PHE A 474 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE A 271 " --> pdb=" O PHE A 474 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 310 through 312 removed outlier: 6.476A pdb=" N TYR A 310 " --> pdb=" O ILE A 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 382 through 384 Processing sheet with id=AA6, first strand: chain 'A' and resid 661 through 663 removed outlier: 3.547A pdb=" N ALA A 647 " --> pdb=" O LEU A 933 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 683 through 686 removed outlier: 3.724A pdb=" N SER A 702 " --> pdb=" O THR A 693 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 746 through 748 removed outlier: 4.449A pdb=" N TYR A 722 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN A 721 " --> pdb=" O ASP A 806 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 891 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL A 805 " --> pdb=" O SER A 889 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N SER A 889 " --> pdb=" O VAL A 805 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU A 807 " --> pdb=" O ARG A 887 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG A 887 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLY A 866 " --> pdb=" O SER A 889 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 750 through 757 removed outlier: 6.434A pdb=" N GLY A 750 " --> pdb=" O ALA A 769 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ALA A 769 " --> pdb=" O GLY A 750 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE A 752 " --> pdb=" O HIS A 767 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N HIS A 767 " --> pdb=" O ILE A 752 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER A 754 " --> pdb=" O HIS A 765 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 774 " --> pdb=" O ASP A 795 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE A 847 " --> pdb=" O ASP A 819 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLY A 851 " --> pdb=" O GLN A 815 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLN A 815 " --> pdb=" O GLY A 851 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 943 through 949 removed outlier: 6.764A pdb=" N ASP A 980 " --> pdb=" O VAL A 948 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A1023 " --> pdb=" O LEU A 983 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 952 through 959 removed outlier: 6.588A pdb=" N ARG A 970 " --> pdb=" O ASP A 955 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N MET A 957 " --> pdb=" O ILE A 968 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE A 968 " --> pdb=" O MET A 957 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 27 through 30 removed outlier: 6.635A pdb=" N LEU B 193 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLN B 30 " --> pdb=" O ALA B 191 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ALA B 191 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER B 190 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 60 through 62 removed outlier: 4.404A pdb=" N VAL B 33 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 469 through 474 removed outlier: 6.439A pdb=" N ASN B 267 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU B 472 " --> pdb=" O ASN B 267 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N SER B 269 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE B 474 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE B 271 " --> pdb=" O PHE B 474 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 310 through 312 removed outlier: 6.475A pdb=" N TYR B 310 " --> pdb=" O ILE B 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 382 through 384 Processing sheet with id=AB8, first strand: chain 'B' and resid 661 through 663 removed outlier: 3.547A pdb=" N ALA B 647 " --> pdb=" O LEU B 933 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 683 through 686 removed outlier: 3.723A pdb=" N SER B 702 " --> pdb=" O THR B 693 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 746 through 748 removed outlier: 4.463A pdb=" N TYR B 722 " --> pdb=" O VAL B 748 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN B 721 " --> pdb=" O ASP B 806 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 891 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL B 805 " --> pdb=" O SER B 889 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N SER B 889 " --> pdb=" O VAL B 805 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU B 807 " --> pdb=" O ARG B 887 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ARG B 887 " --> pdb=" O LEU B 807 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLY B 866 " --> pdb=" O SER B 889 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 750 through 757 removed outlier: 6.687A pdb=" N HIS B 765 " --> pdb=" O GLU B 753 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL B 755 " --> pdb=" O GLN B 763 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLN B 763 " --> pdb=" O VAL B 755 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 774 " --> pdb=" O ASP B 795 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE B 847 " --> pdb=" O ASP B 819 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLY B 851 " --> pdb=" O GLN B 815 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLN B 815 " --> pdb=" O GLY B 851 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 943 through 949 removed outlier: 6.764A pdb=" N ASP B 980 " --> pdb=" O VAL B 948 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B1023 " --> pdb=" O LEU B 983 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 952 through 959 removed outlier: 6.588A pdb=" N ARG B 970 " --> pdb=" O ASP B 955 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N MET B 957 " --> pdb=" O ILE B 968 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE B 968 " --> pdb=" O MET B 957 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 27 through 30 removed outlier: 6.631A pdb=" N LEU C 193 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLN C 30 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ALA C 191 " --> pdb=" O GLN C 30 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER C 190 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 60 through 62 removed outlier: 4.400A pdb=" N VAL C 33 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR C 120 " --> pdb=" O ARG C 116 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 469 through 474 removed outlier: 6.444A pdb=" N ASN C 267 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU C 472 " --> pdb=" O ASN C 267 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N SER C 269 " --> pdb=" O LEU C 472 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N PHE C 474 " --> pdb=" O SER C 269 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE C 271 " --> pdb=" O PHE C 474 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 310 through 312 removed outlier: 6.480A pdb=" N TYR C 310 " --> pdb=" O ILE C 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 382 through 384 Processing sheet with id=AD1, first strand: chain 'C' and resid 661 through 663 removed outlier: 3.504A pdb=" N ALA C 647 " --> pdb=" O LEU C 933 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 683 through 686 removed outlier: 3.728A pdb=" N SER C 702 " --> pdb=" O THR C 693 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 746 through 748 removed outlier: 4.461A pdb=" N TYR C 722 " --> pdb=" O VAL C 748 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN C 721 " --> pdb=" O ASP C 806 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 891 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL C 805 " --> pdb=" O SER C 889 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N SER C 889 " --> pdb=" O VAL C 805 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU C 807 " --> pdb=" O ARG C 887 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ARG C 887 " --> pdb=" O LEU C 807 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLY C 866 " --> pdb=" O SER C 889 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 750 through 757 removed outlier: 6.442A pdb=" N GLY C 750 " --> pdb=" O ALA C 769 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ALA C 769 " --> pdb=" O GLY C 750 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE C 752 " --> pdb=" O HIS C 767 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N HIS C 767 " --> pdb=" O ILE C 752 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER C 754 " --> pdb=" O HIS C 765 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 774 " --> pdb=" O ASP C 795 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N PHE C 847 " --> pdb=" O ASP C 819 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N GLY C 851 " --> pdb=" O GLN C 815 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN C 815 " --> pdb=" O GLY C 851 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 943 through 949 removed outlier: 6.764A pdb=" N ASP C 980 " --> pdb=" O VAL C 948 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA C1023 " --> pdb=" O LEU C 983 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 952 through 959 removed outlier: 6.591A pdb=" N ARG C 970 " --> pdb=" O ASP C 955 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET C 957 " --> pdb=" O ILE C 968 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE C 968 " --> pdb=" O MET C 957 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 27 through 30 removed outlier: 6.633A pdb=" N LEU D 193 " --> pdb=" O ILE D 28 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN D 30 " --> pdb=" O ALA D 191 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ALA D 191 " --> pdb=" O GLN D 30 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER D 190 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 60 through 62 removed outlier: 4.402A pdb=" N VAL D 33 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 469 through 474 removed outlier: 6.439A pdb=" N ASN D 267 " --> pdb=" O SER D 470 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU D 472 " --> pdb=" O ASN D 267 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N SER D 269 " --> pdb=" O LEU D 472 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE D 474 " --> pdb=" O SER D 269 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE D 271 " --> pdb=" O PHE D 474 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 310 through 312 removed outlier: 6.475A pdb=" N TYR D 310 " --> pdb=" O ILE D 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'D' and resid 382 through 384 Processing sheet with id=AE3, first strand: chain 'D' and resid 661 through 663 removed outlier: 3.546A pdb=" N ALA D 647 " --> pdb=" O LEU D 933 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 683 through 686 removed outlier: 3.733A pdb=" N SER D 702 " --> pdb=" O THR D 693 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 746 through 748 removed outlier: 4.451A pdb=" N TYR D 722 " --> pdb=" O VAL D 748 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN D 721 " --> pdb=" O ASP D 806 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU D 891 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL D 805 " --> pdb=" O SER D 889 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N SER D 889 " --> pdb=" O VAL D 805 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU D 807 " --> pdb=" O ARG D 887 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ARG D 887 " --> pdb=" O LEU D 807 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLY D 866 " --> pdb=" O SER D 889 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 750 through 757 removed outlier: 6.442A pdb=" N GLY D 750 " --> pdb=" O ALA D 769 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ALA D 769 " --> pdb=" O GLY D 750 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ILE D 752 " --> pdb=" O HIS D 767 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N HIS D 767 " --> pdb=" O ILE D 752 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER D 754 " --> pdb=" O HIS D 765 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL D 774 " --> pdb=" O ASP D 795 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N PHE D 847 " --> pdb=" O ASP D 819 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLY D 851 " --> pdb=" O GLN D 815 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLN D 815 " --> pdb=" O GLY D 851 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 943 through 949 removed outlier: 6.764A pdb=" N ASP D 980 " --> pdb=" O VAL D 948 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA D1023 " --> pdb=" O LEU D 983 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 952 through 959 removed outlier: 6.588A pdb=" N ARG D 970 " --> pdb=" O ASP D 955 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N MET D 957 " --> pdb=" O ILE D 968 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE D 968 " --> pdb=" O MET D 957 " (cutoff:3.500A) 1435 hydrogen bonds defined for protein. 4026 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: 7.84 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5676 1.30 - 1.42: 8696 1.42 - 1.55: 18812 1.55 - 1.68: 0 1.68 - 1.81: 188 Bond restraints: 33372 Sorted by residual: bond pdb=" C HIS A 597 " pdb=" O HIS A 597 " ideal model delta sigma weight residual 1.235 1.166 0.069 1.26e-02 6.30e+03 2.99e+01 bond pdb=" C HIS B 597 " pdb=" O HIS B 597 " ideal model delta sigma weight residual 1.235 1.167 0.069 1.26e-02 6.30e+03 2.96e+01 bond pdb=" C HIS C 597 " pdb=" O HIS C 597 " ideal model delta sigma weight residual 1.235 1.167 0.068 1.26e-02 6.30e+03 2.95e+01 bond pdb=" C HIS D 597 " pdb=" O HIS D 597 " ideal model delta sigma weight residual 1.235 1.167 0.068 1.26e-02 6.30e+03 2.93e+01 bond pdb=" C PHE D 596 " pdb=" O PHE D 596 " ideal model delta sigma weight residual 1.233 1.168 0.066 1.28e-02 6.10e+03 2.64e+01 ... (remaining 33367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 44924 2.79 - 5.57: 412 5.57 - 8.36: 88 8.36 - 11.14: 4 11.14 - 13.93: 4 Bond angle restraints: 45432 Sorted by residual: angle pdb=" CA ASP B 387 " pdb=" CB ASP B 387 " pdb=" CG ASP B 387 " ideal model delta sigma weight residual 112.60 123.07 -10.47 1.00e+00 1.00e+00 1.10e+02 angle pdb=" CA ASP D 387 " pdb=" CB ASP D 387 " pdb=" CG ASP D 387 " ideal model delta sigma weight residual 112.60 123.05 -10.45 1.00e+00 1.00e+00 1.09e+02 angle pdb=" CA ASP A 387 " pdb=" CB ASP A 387 " pdb=" CG ASP A 387 " ideal model delta sigma weight residual 112.60 122.99 -10.39 1.00e+00 1.00e+00 1.08e+02 angle pdb=" CA ASP C 387 " pdb=" CB ASP C 387 " pdb=" CG ASP C 387 " ideal model delta sigma weight residual 112.60 122.96 -10.36 1.00e+00 1.00e+00 1.07e+02 angle pdb=" C ASP C 919 " pdb=" CA ASP C 919 " pdb=" CB ASP C 919 " ideal model delta sigma weight residual 110.88 96.95 13.93 1.57e+00 4.06e-01 7.87e+01 ... (remaining 45427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 18031 18.01 - 36.01: 1465 36.01 - 54.02: 233 54.02 - 72.03: 36 72.03 - 90.04: 27 Dihedral angle restraints: 19792 sinusoidal: 7836 harmonic: 11956 Sorted by residual: dihedral pdb=" C ASP B 919 " pdb=" N ASP B 919 " pdb=" CA ASP B 919 " pdb=" CB ASP B 919 " ideal model delta harmonic sigma weight residual -122.60 -104.29 -18.31 0 2.50e+00 1.60e-01 5.36e+01 dihedral pdb=" C ASP C 919 " pdb=" N ASP C 919 " pdb=" CA ASP C 919 " pdb=" CB ASP C 919 " ideal model delta harmonic sigma weight residual -122.60 -104.33 -18.27 0 2.50e+00 1.60e-01 5.34e+01 dihedral pdb=" C ASP D 919 " pdb=" N ASP D 919 " pdb=" CA ASP D 919 " pdb=" CB ASP D 919 " ideal model delta harmonic sigma weight residual -122.60 -104.36 -18.24 0 2.50e+00 1.60e-01 5.33e+01 ... (remaining 19789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4569 0.098 - 0.196: 299 0.196 - 0.294: 4 0.294 - 0.392: 8 0.392 - 0.490: 8 Chirality restraints: 4888 Sorted by residual: chirality pdb=" CA ARG C 116 " pdb=" N ARG C 116 " pdb=" C ARG C 116 " pdb=" CB ARG C 116 " both_signs ideal model delta sigma weight residual False 2.51 3.00 -0.49 2.00e-01 2.50e+01 6.01e+00 chirality pdb=" CA ARG A 116 " pdb=" N ARG A 116 " pdb=" C ARG A 116 " pdb=" CB ARG A 116 " both_signs ideal model delta sigma weight residual False 2.51 3.00 -0.49 2.00e-01 2.50e+01 5.93e+00 chirality pdb=" CA ARG B 116 " pdb=" N ARG B 116 " pdb=" C ARG B 116 " pdb=" CB ARG B 116 " both_signs ideal model delta sigma weight residual False 2.51 2.99 -0.48 2.00e-01 2.50e+01 5.77e+00 ... (remaining 4885 not shown) Planarity restraints: 6020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 387 " 0.023 2.00e-02 2.50e+03 4.60e-02 2.11e+01 pdb=" C ASP A 387 " -0.080 2.00e-02 2.50e+03 pdb=" O ASP A 387 " 0.029 2.00e-02 2.50e+03 pdb=" N SER A 388 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 387 " -0.023 2.00e-02 2.50e+03 4.59e-02 2.11e+01 pdb=" C ASP B 387 " 0.079 2.00e-02 2.50e+03 pdb=" O ASP B 387 " -0.029 2.00e-02 2.50e+03 pdb=" N SER B 388 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 387 " 0.022 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" C ASP C 387 " -0.079 2.00e-02 2.50e+03 pdb=" O ASP C 387 " 0.028 2.00e-02 2.50e+03 pdb=" N SER C 388 " 0.028 2.00e-02 2.50e+03 ... (remaining 6017 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 196 2.57 - 3.16: 24543 3.16 - 3.74: 48842 3.74 - 4.32: 71603 4.32 - 4.90: 122563 Nonbonded interactions: 267747 Sorted by model distance: nonbonded pdb=" OD2 ASP D 387 " pdb="ZN ZN D1101 " model vdw 1.992 2.230 nonbonded pdb=" OD2 ASP B 387 " pdb="ZN ZN B1101 " model vdw 1.993 2.230 nonbonded pdb=" OD2 ASP C 387 " pdb="ZN ZN C1101 " model vdw 1.995 2.230 nonbonded pdb=" OD2 ASP A 387 " pdb="ZN ZN A1101 " model vdw 2.001 2.230 nonbonded pdb=" OD1 ASP A 277 " pdb="ZN ZN A1101 " model vdw 2.094 2.230 ... (remaining 267742 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 33.830 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 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 : 0.005 0.255 33380 Z= 0.272 Angle : 0.705 13.926 45432 Z= 0.427 Chirality : 0.051 0.490 4888 Planarity : 0.005 0.046 6020 Dihedral : 13.481 90.035 12112 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.13), residues: 4144 helix: 1.57 (0.15), residues: 1208 sheet: -0.17 (0.15), residues: 1104 loop : -2.03 (0.13), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 826 TYR 0.019 0.001 TYR A 87 PHE 0.028 0.002 PHE B 596 TRP 0.013 0.002 TRP A 72 HIS 0.022 0.001 HIS A 597 Details of bonding type rmsd covalent geometry : bond 0.00438 (33372) covalent geometry : angle 0.70478 (45432) hydrogen bonds : bond 0.14688 ( 1435) hydrogen bonds : angle 5.31453 ( 4026) metal coordination : bond 0.18644 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 1.325 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.7879 time to fit residues: 470.6470 Evaluate side-chains 352 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS A 555 GLN A 765 HIS A 767 HIS A1018 GLN B 109 HIS B 555 GLN B1018 GLN C 109 HIS C 555 GLN C 765 HIS C 767 HIS C1018 GLN D 109 HIS D 555 GLN D 765 HIS D 767 HIS D1018 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.122044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.104381 restraints weight = 42732.584| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.88 r_work: 0.3045 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 33380 Z= 0.115 Angle : 0.560 7.044 45432 Z= 0.299 Chirality : 0.044 0.169 4888 Planarity : 0.004 0.035 6020 Dihedral : 4.870 27.416 4532 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.53 % Allowed : 8.96 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.13), residues: 4144 helix: 1.88 (0.15), residues: 1216 sheet: -0.02 (0.16), residues: 1072 loop : -1.87 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 78 TYR 0.014 0.001 TYR A 87 PHE 0.017 0.001 PHE A 847 TRP 0.011 0.001 TRP A 72 HIS 0.008 0.001 HIS C 597 Details of bonding type rmsd covalent geometry : bond 0.00246 (33372) covalent geometry : angle 0.56012 (45432) hydrogen bonds : bond 0.04470 ( 1435) hydrogen bonds : angle 4.41834 ( 4026) metal coordination : bond 0.00693 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 386 time to evaluate : 1.183 Fit side-chains REVERT: A 10 GLU cc_start: 0.8271 (tp30) cc_final: 0.8012 (tp30) REVERT: A 198 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7568 (pt0) REVERT: A 416 ASP cc_start: 0.7657 (m-30) cc_final: 0.7427 (m-30) REVERT: A 923 ASP cc_start: 0.8601 (t70) cc_final: 0.8362 (t70) REVERT: B 10 GLU cc_start: 0.8295 (tp30) cc_final: 0.8038 (tp30) REVERT: B 198 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7569 (pt0) REVERT: B 416 ASP cc_start: 0.7661 (m-30) cc_final: 0.7442 (m-30) REVERT: B 756 ASN cc_start: 0.7740 (m-40) cc_final: 0.7365 (m110) REVERT: B 923 ASP cc_start: 0.8595 (t70) cc_final: 0.8360 (t70) REVERT: C 10 GLU cc_start: 0.8280 (tp30) cc_final: 0.8020 (tp30) REVERT: C 198 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7583 (pt0) REVERT: C 416 ASP cc_start: 0.7662 (m-30) cc_final: 0.7444 (m-30) REVERT: C 635 ARG cc_start: 0.7575 (ttp-110) cc_final: 0.7369 (ttp-110) REVERT: C 923 ASP cc_start: 0.8659 (t70) cc_final: 0.8441 (t70) REVERT: D 10 GLU cc_start: 0.8285 (tp30) cc_final: 0.8030 (tp30) REVERT: D 198 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7600 (pt0) REVERT: D 416 ASP cc_start: 0.7694 (m-30) cc_final: 0.7490 (m-30) REVERT: D 923 ASP cc_start: 0.8604 (t70) cc_final: 0.8363 (t70) outliers start: 52 outliers final: 16 residues processed: 415 average time/residue: 0.7083 time to fit residues: 346.3758 Evaluate side-chains 385 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 365 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 640 GLN Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 548 ASP Chi-restraints excluded: chain C residue 640 GLN Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 640 GLN Chi-restraints excluded: chain D residue 1005 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 130 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 258 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 195 optimal weight: 0.9980 chunk 237 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 182 optimal weight: 10.0000 chunk 377 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS B 109 HIS B 759 ASN C 109 HIS D 109 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.115372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.097660 restraints weight = 43149.754| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.87 r_work: 0.2990 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 33380 Z= 0.294 Angle : 0.701 7.601 45432 Z= 0.377 Chirality : 0.051 0.181 4888 Planarity : 0.006 0.052 6020 Dihedral : 5.541 28.589 4532 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.24 % Allowed : 11.06 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.13), residues: 4144 helix: 1.52 (0.15), residues: 1224 sheet: -0.29 (0.15), residues: 1168 loop : -2.06 (0.13), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 17 TYR 0.027 0.002 TYR A 87 PHE 0.029 0.003 PHE C 652 TRP 0.016 0.002 TRP C 72 HIS 0.012 0.001 HIS C 597 Details of bonding type rmsd covalent geometry : bond 0.00703 (33372) covalent geometry : angle 0.70092 (45432) hydrogen bonds : bond 0.06744 ( 1435) hydrogen bonds : angle 4.57356 ( 4026) metal coordination : bond 0.00137 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 367 time to evaluate : 1.129 Fit side-chains REVERT: A 10 GLU cc_start: 0.8396 (tp30) cc_final: 0.8106 (tp30) REVERT: A 198 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7784 (pt0) REVERT: A 728 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8357 (mt-10) REVERT: A 756 ASN cc_start: 0.7809 (m-40) cc_final: 0.7411 (m110) REVERT: A 763 GLN cc_start: 0.8522 (mt0) cc_final: 0.8059 (mt0) REVERT: A 923 ASP cc_start: 0.8811 (t70) cc_final: 0.8510 (t70) REVERT: B 10 GLU cc_start: 0.8411 (tp30) cc_final: 0.8121 (tp30) REVERT: B 198 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7800 (pt0) REVERT: B 615 ASP cc_start: 0.8091 (m-30) cc_final: 0.7819 (m-30) REVERT: B 728 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8386 (mt-10) REVERT: B 756 ASN cc_start: 0.8072 (m-40) cc_final: 0.7728 (m110) REVERT: B 923 ASP cc_start: 0.8811 (t70) cc_final: 0.8508 (t70) REVERT: C 10 GLU cc_start: 0.8389 (tp30) cc_final: 0.8093 (tp30) REVERT: C 198 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7772 (pt0) REVERT: C 728 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8362 (mt-10) REVERT: C 756 ASN cc_start: 0.7762 (m110) cc_final: 0.7438 (m110) REVERT: C 923 ASP cc_start: 0.8814 (t70) cc_final: 0.8560 (t70) REVERT: D 10 GLU cc_start: 0.8403 (tp30) cc_final: 0.8112 (tp30) REVERT: D 198 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7820 (pt0) REVERT: D 728 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8367 (mt-10) REVERT: D 756 ASN cc_start: 0.7765 (m110) cc_final: 0.7443 (m110) REVERT: D 923 ASP cc_start: 0.8817 (t70) cc_final: 0.8515 (t70) outliers start: 76 outliers final: 34 residues processed: 408 average time/residue: 0.7134 time to fit residues: 343.5787 Evaluate side-chains 382 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 344 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 640 GLN Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 982 MET Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 548 ASP Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 640 GLN Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 982 MET Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 640 GLN Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 982 MET Chi-restraints excluded: chain D residue 1005 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 226 optimal weight: 0.9990 chunk 188 optimal weight: 6.9990 chunk 273 optimal weight: 0.7980 chunk 142 optimal weight: 0.6980 chunk 388 optimal weight: 7.9990 chunk 216 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 320 optimal weight: 2.9990 chunk 407 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 326 optimal weight: 0.2980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS B 109 HIS C 109 HIS D 109 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.120668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.102985 restraints weight = 42562.633| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.88 r_work: 0.3026 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33380 Z= 0.121 Angle : 0.553 6.536 45432 Z= 0.297 Chirality : 0.044 0.157 4888 Planarity : 0.004 0.037 6020 Dihedral : 5.051 27.133 4532 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.74 % Allowed : 13.33 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.13), residues: 4144 helix: 1.82 (0.15), residues: 1220 sheet: -0.06 (0.16), residues: 1080 loop : -1.99 (0.13), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.016 0.001 TYR C 87 PHE 0.020 0.001 PHE A 847 TRP 0.014 0.001 TRP C 72 HIS 0.009 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00269 (33372) covalent geometry : angle 0.55332 (45432) hydrogen bonds : bond 0.04517 ( 1435) hydrogen bonds : angle 4.34619 ( 4026) metal coordination : bond 0.00107 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 376 time to evaluate : 1.197 Fit side-chains REVERT: A 10 GLU cc_start: 0.8279 (tp30) cc_final: 0.7876 (tp30) REVERT: A 198 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7709 (pt0) REVERT: A 615 ASP cc_start: 0.7948 (m-30) cc_final: 0.7649 (m-30) REVERT: A 923 ASP cc_start: 0.8733 (t70) cc_final: 0.8438 (t70) REVERT: B 10 GLU cc_start: 0.8273 (tp30) cc_final: 0.7867 (tp30) REVERT: B 198 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7676 (pt0) REVERT: B 753 GLU cc_start: 0.7504 (mp0) cc_final: 0.7304 (mp0) REVERT: B 756 ASN cc_start: 0.7974 (m-40) cc_final: 0.7599 (m110) REVERT: B 923 ASP cc_start: 0.8732 (t70) cc_final: 0.8437 (t70) REVERT: C 10 GLU cc_start: 0.8281 (tp30) cc_final: 0.7875 (tp30) REVERT: C 198 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7667 (pt0) REVERT: C 615 ASP cc_start: 0.7939 (m-30) cc_final: 0.7649 (m-30) REVERT: C 923 ASP cc_start: 0.8730 (t70) cc_final: 0.8470 (t70) REVERT: D 10 GLU cc_start: 0.8271 (tp30) cc_final: 0.7871 (tp30) REVERT: D 198 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7710 (pt0) REVERT: D 615 ASP cc_start: 0.7959 (m-30) cc_final: 0.7668 (m-30) REVERT: D 923 ASP cc_start: 0.8742 (t70) cc_final: 0.8445 (t70) outliers start: 59 outliers final: 27 residues processed: 412 average time/residue: 0.6871 time to fit residues: 335.0354 Evaluate side-chains 394 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 363 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 640 GLN Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 548 ASP Chi-restraints excluded: chain C residue 640 GLN Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 640 GLN Chi-restraints excluded: chain D residue 689 VAL Chi-restraints excluded: chain D residue 1005 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 310 optimal weight: 1.9990 chunk 325 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 97 optimal weight: 0.0470 chunk 230 optimal weight: 5.9990 chunk 286 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 320 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS B 109 HIS C 109 HIS D 109 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.120103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.102465 restraints weight = 42536.503| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.87 r_work: 0.3019 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 33380 Z= 0.136 Angle : 0.560 6.607 45432 Z= 0.301 Chirality : 0.044 0.152 4888 Planarity : 0.004 0.037 6020 Dihedral : 4.967 26.070 4532 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.95 % Allowed : 14.65 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.13), residues: 4144 helix: 1.99 (0.15), residues: 1212 sheet: -0.06 (0.16), residues: 1088 loop : -1.90 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 653 TYR 0.018 0.001 TYR A 87 PHE 0.020 0.002 PHE A 847 TRP 0.012 0.001 TRP C 72 HIS 0.009 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00311 (33372) covalent geometry : angle 0.55993 (45432) hydrogen bonds : bond 0.04650 ( 1435) hydrogen bonds : angle 4.27010 ( 4026) metal coordination : bond 0.00112 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 368 time to evaluate : 1.062 Fit side-chains REVERT: A 10 GLU cc_start: 0.8251 (tp30) cc_final: 0.7826 (tp30) REVERT: A 198 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7809 (pt0) REVERT: A 208 ASP cc_start: 0.8683 (t0) cc_final: 0.8447 (t0) REVERT: A 728 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8360 (mt-10) REVERT: A 923 ASP cc_start: 0.8731 (t70) cc_final: 0.8427 (t70) REVERT: B 10 GLU cc_start: 0.8259 (tp30) cc_final: 0.7834 (tp30) REVERT: B 198 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7790 (pt0) REVERT: B 208 ASP cc_start: 0.8677 (t0) cc_final: 0.8444 (t0) REVERT: B 611 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8073 (mm-30) REVERT: B 615 ASP cc_start: 0.7907 (m-30) cc_final: 0.7656 (m-30) REVERT: B 728 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8375 (mt-10) REVERT: B 753 GLU cc_start: 0.7512 (mp0) cc_final: 0.7243 (mp0) REVERT: B 756 ASN cc_start: 0.8000 (m-40) cc_final: 0.7614 (m110) REVERT: B 923 ASP cc_start: 0.8733 (t70) cc_final: 0.8423 (t70) REVERT: C 10 GLU cc_start: 0.8257 (tp30) cc_final: 0.7830 (tp30) REVERT: C 198 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7781 (pt0) REVERT: C 208 ASP cc_start: 0.8684 (t0) cc_final: 0.8447 (t0) REVERT: C 728 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8378 (mt-10) REVERT: C 923 ASP cc_start: 0.8728 (t70) cc_final: 0.8477 (t70) REVERT: D 10 GLU cc_start: 0.8251 (tp30) cc_final: 0.7827 (tp30) REVERT: D 198 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7819 (pt0) REVERT: D 208 ASP cc_start: 0.8688 (t0) cc_final: 0.8451 (t0) REVERT: D 728 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8373 (mt-10) REVERT: D 923 ASP cc_start: 0.8737 (t70) cc_final: 0.8428 (t70) outliers start: 66 outliers final: 38 residues processed: 408 average time/residue: 0.6873 time to fit residues: 332.3846 Evaluate side-chains 392 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 350 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 640 GLN Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 982 MET Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 548 ASP Chi-restraints excluded: chain C residue 640 GLN Chi-restraints excluded: chain C residue 982 MET Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 640 GLN Chi-restraints excluded: chain D residue 689 VAL Chi-restraints excluded: chain D residue 982 MET Chi-restraints excluded: chain D residue 1005 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 30 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 365 optimal weight: 4.9990 chunk 276 optimal weight: 7.9990 chunk 331 optimal weight: 0.8980 chunk 311 optimal weight: 3.9990 chunk 371 optimal weight: 0.7980 chunk 296 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 289 optimal weight: 0.0970 chunk 87 optimal weight: 3.9990 overall best weight: 1.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS B 109 HIS C 109 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.121338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.103539 restraints weight = 42462.341| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.88 r_work: 0.3033 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 33380 Z= 0.122 Angle : 0.542 6.515 45432 Z= 0.291 Chirality : 0.043 0.147 4888 Planarity : 0.004 0.036 6020 Dihedral : 4.860 25.835 4532 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.59 % Allowed : 15.51 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.13), residues: 4144 helix: 2.09 (0.15), residues: 1212 sheet: -0.04 (0.15), residues: 1088 loop : -1.86 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 635 TYR 0.016 0.001 TYR A 87 PHE 0.020 0.001 PHE D 847 TRP 0.012 0.001 TRP A 72 HIS 0.008 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00274 (33372) covalent geometry : angle 0.54226 (45432) hydrogen bonds : bond 0.04334 ( 1435) hydrogen bonds : angle 4.22154 ( 4026) metal coordination : bond 0.00107 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 378 time to evaluate : 1.339 Fit side-chains REVERT: A 10 GLU cc_start: 0.8217 (tp30) cc_final: 0.7796 (tp30) REVERT: A 198 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7703 (pt0) REVERT: A 615 ASP cc_start: 0.7863 (m-30) cc_final: 0.7618 (m-30) REVERT: A 728 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8343 (mt-10) REVERT: A 923 ASP cc_start: 0.8719 (t70) cc_final: 0.8400 (t70) REVERT: B 10 GLU cc_start: 0.8223 (tp30) cc_final: 0.7801 (tp30) REVERT: B 198 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7693 (pt0) REVERT: B 728 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8356 (mt-10) REVERT: B 753 GLU cc_start: 0.7541 (mp0) cc_final: 0.7190 (mp0) REVERT: B 756 ASN cc_start: 0.7974 (m-40) cc_final: 0.7593 (m110) REVERT: B 923 ASP cc_start: 0.8726 (t70) cc_final: 0.8401 (t70) REVERT: C 10 GLU cc_start: 0.8225 (tp30) cc_final: 0.7799 (tp30) REVERT: C 198 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7662 (pt0) REVERT: C 615 ASP cc_start: 0.7864 (m-30) cc_final: 0.7607 (m-30) REVERT: C 728 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8366 (mt-10) REVERT: C 923 ASP cc_start: 0.8716 (t70) cc_final: 0.8458 (t70) REVERT: D 10 GLU cc_start: 0.8222 (tp30) cc_final: 0.7802 (tp30) REVERT: D 198 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7712 (pt0) REVERT: D 615 ASP cc_start: 0.7883 (m-30) cc_final: 0.7638 (m-30) REVERT: D 704 LEU cc_start: 0.8442 (tm) cc_final: 0.8202 (tm) REVERT: D 728 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8366 (mt-10) REVERT: D 923 ASP cc_start: 0.8730 (t70) cc_final: 0.8407 (t70) outliers start: 54 outliers final: 35 residues processed: 413 average time/residue: 0.6817 time to fit residues: 334.0447 Evaluate side-chains 388 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 349 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 640 GLN Chi-restraints excluded: chain A residue 680 ASN Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 548 ASP Chi-restraints excluded: chain C residue 640 GLN Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 640 GLN Chi-restraints excluded: chain D residue 689 VAL Chi-restraints excluded: chain D residue 787 THR Chi-restraints excluded: chain D residue 1005 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 178 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 325 optimal weight: 0.0980 chunk 67 optimal weight: 7.9990 chunk 407 optimal weight: 0.0670 chunk 330 optimal weight: 4.9990 chunk 273 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 102 optimal weight: 8.9990 chunk 236 optimal weight: 0.9990 chunk 276 optimal weight: 8.9990 overall best weight: 1.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 HIS C 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.122071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.104199 restraints weight = 42585.294| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.89 r_work: 0.3040 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33380 Z= 0.119 Angle : 0.540 6.505 45432 Z= 0.289 Chirality : 0.043 0.168 4888 Planarity : 0.004 0.036 6020 Dihedral : 4.780 25.492 4532 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.30 % Allowed : 15.15 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.13), residues: 4144 helix: 2.19 (0.15), residues: 1212 sheet: -0.07 (0.15), residues: 1096 loop : -1.81 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 653 TYR 0.016 0.001 TYR A 87 PHE 0.020 0.001 PHE C 847 TRP 0.011 0.001 TRP D 72 HIS 0.008 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00267 (33372) covalent geometry : angle 0.54011 (45432) hydrogen bonds : bond 0.04199 ( 1435) hydrogen bonds : angle 4.17674 ( 4026) metal coordination : bond 0.00099 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 370 time to evaluate : 1.275 Fit side-chains REVERT: A 10 GLU cc_start: 0.8212 (tp30) cc_final: 0.7779 (tp30) REVERT: A 198 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7694 (pt0) REVERT: A 615 ASP cc_start: 0.7756 (m-30) cc_final: 0.7503 (m-30) REVERT: A 704 LEU cc_start: 0.8445 (tm) cc_final: 0.8214 (tm) REVERT: A 728 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8347 (mt-10) REVERT: A 923 ASP cc_start: 0.8720 (t70) cc_final: 0.8391 (t70) REVERT: B 10 GLU cc_start: 0.8209 (tp30) cc_final: 0.7773 (tp30) REVERT: B 198 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7694 (pt0) REVERT: B 704 LEU cc_start: 0.8445 (tm) cc_final: 0.8215 (tm) REVERT: B 728 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8356 (mt-10) REVERT: B 756 ASN cc_start: 0.7936 (m-40) cc_final: 0.7553 (m110) REVERT: B 923 ASP cc_start: 0.8717 (t70) cc_final: 0.8383 (t70) REVERT: C 10 GLU cc_start: 0.8214 (tp30) cc_final: 0.7777 (tp30) REVERT: C 198 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7677 (pt0) REVERT: C 704 LEU cc_start: 0.8443 (tm) cc_final: 0.8209 (tm) REVERT: C 728 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8363 (mt-10) REVERT: C 923 ASP cc_start: 0.8708 (t70) cc_final: 0.8445 (t70) REVERT: D 10 GLU cc_start: 0.8218 (tp30) cc_final: 0.7786 (tp30) REVERT: D 198 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7721 (pt0) REVERT: D 615 ASP cc_start: 0.7795 (m-30) cc_final: 0.7544 (m-30) REVERT: D 704 LEU cc_start: 0.8442 (tm) cc_final: 0.8196 (tm) REVERT: D 728 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8363 (mt-10) REVERT: D 923 ASP cc_start: 0.8714 (t70) cc_final: 0.8379 (t70) outliers start: 78 outliers final: 38 residues processed: 427 average time/residue: 0.6747 time to fit residues: 342.7386 Evaluate side-chains 389 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 347 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 982 MET Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 548 ASP Chi-restraints excluded: chain C residue 640 GLN Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 982 MET Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 689 VAL Chi-restraints excluded: chain D residue 787 THR Chi-restraints excluded: chain D residue 982 MET Chi-restraints excluded: chain D residue 1005 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 327 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 352 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 245 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 298 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.119090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.101141 restraints weight = 42267.452| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.88 r_work: 0.2995 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 33380 Z= 0.164 Angle : 0.582 6.745 45432 Z= 0.313 Chirality : 0.045 0.188 4888 Planarity : 0.004 0.037 6020 Dihedral : 4.990 26.230 4532 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.18 % Allowed : 15.62 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.30 (0.13), residues: 4144 helix: 2.05 (0.15), residues: 1220 sheet: -0.10 (0.15), residues: 1104 loop : -1.91 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 653 TYR 0.020 0.002 TYR C 87 PHE 0.021 0.002 PHE C 847 TRP 0.011 0.002 TRP D 406 HIS 0.008 0.001 HIS C 597 Details of bonding type rmsd covalent geometry : bond 0.00384 (33372) covalent geometry : angle 0.58247 (45432) hydrogen bonds : bond 0.04952 ( 1435) hydrogen bonds : angle 4.26266 ( 4026) metal coordination : bond 0.00141 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 364 time to evaluate : 1.164 Fit side-chains REVERT: A 10 GLU cc_start: 0.8192 (tp30) cc_final: 0.7754 (tp30) REVERT: A 113 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8531 (tt) REVERT: A 198 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7706 (pt0) REVERT: A 208 ASP cc_start: 0.8620 (t0) cc_final: 0.8316 (t0) REVERT: A 615 ASP cc_start: 0.7863 (m-30) cc_final: 0.7593 (m-30) REVERT: A 728 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8344 (mt-10) REVERT: A 923 ASP cc_start: 0.8739 (t70) cc_final: 0.8405 (t70) REVERT: B 10 GLU cc_start: 0.8207 (tp30) cc_final: 0.7769 (tp30) REVERT: B 113 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8537 (tt) REVERT: B 198 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7707 (pt0) REVERT: B 208 ASP cc_start: 0.8622 (t0) cc_final: 0.8323 (t0) REVERT: B 728 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8333 (mt-10) REVERT: B 756 ASN cc_start: 0.7987 (m-40) cc_final: 0.7612 (m110) REVERT: B 923 ASP cc_start: 0.8724 (t70) cc_final: 0.8389 (t70) REVERT: C 10 GLU cc_start: 0.8195 (tp30) cc_final: 0.7758 (tp30) REVERT: C 113 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8567 (tt) REVERT: C 198 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7701 (pt0) REVERT: C 208 ASP cc_start: 0.8625 (t0) cc_final: 0.8319 (t0) REVERT: C 728 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8329 (mt-10) REVERT: C 756 ASN cc_start: 0.7695 (m110) cc_final: 0.7336 (m110) REVERT: C 923 ASP cc_start: 0.8734 (t70) cc_final: 0.8450 (t70) REVERT: D 10 GLU cc_start: 0.8203 (tp30) cc_final: 0.7771 (tp30) REVERT: D 113 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8537 (tt) REVERT: D 198 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7684 (pt0) REVERT: D 208 ASP cc_start: 0.8616 (t0) cc_final: 0.8315 (t0) REVERT: D 611 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8042 (mm-30) REVERT: D 615 ASP cc_start: 0.7876 (m-30) cc_final: 0.7602 (m-30) REVERT: D 728 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8334 (mt-10) REVERT: D 756 ASN cc_start: 0.7706 (m110) cc_final: 0.7347 (m110) REVERT: D 923 ASP cc_start: 0.8724 (t70) cc_final: 0.8391 (t70) outliers start: 74 outliers final: 56 residues processed: 412 average time/residue: 0.6940 time to fit residues: 340.0228 Evaluate side-chains 421 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 357 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 640 GLN Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 947 SER Chi-restraints excluded: chain B residue 982 MET Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 548 ASP Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 640 GLN Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 982 MET Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 640 GLN Chi-restraints excluded: chain D residue 680 ASN Chi-restraints excluded: chain D residue 689 VAL Chi-restraints excluded: chain D residue 723 GLU Chi-restraints excluded: chain D residue 787 THR Chi-restraints excluded: chain D residue 947 SER Chi-restraints excluded: chain D residue 982 MET Chi-restraints excluded: chain D residue 1005 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 14 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 238 optimal weight: 0.8980 chunk 342 optimal weight: 2.9990 chunk 303 optimal weight: 10.0000 chunk 361 optimal weight: 1.9990 chunk 276 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 chunk 296 optimal weight: 0.9980 chunk 338 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 HIS C 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.103019 restraints weight = 42067.464| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.86 r_work: 0.3055 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33380 Z= 0.125 Angle : 0.553 6.498 45432 Z= 0.297 Chirality : 0.044 0.197 4888 Planarity : 0.004 0.036 6020 Dihedral : 4.834 25.740 4532 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.86 % Allowed : 15.92 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.13), residues: 4144 helix: 2.12 (0.15), residues: 1220 sheet: -0.06 (0.15), residues: 1100 loop : -1.86 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 653 TYR 0.017 0.001 TYR B 87 PHE 0.019 0.001 PHE C 847 TRP 0.012 0.001 TRP B 72 HIS 0.008 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00283 (33372) covalent geometry : angle 0.55305 (45432) hydrogen bonds : bond 0.04310 ( 1435) hydrogen bonds : angle 4.20904 ( 4026) metal coordination : bond 0.00119 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 367 time to evaluate : 1.315 Fit side-chains REVERT: A 10 GLU cc_start: 0.8232 (tp30) cc_final: 0.7813 (tp30) REVERT: A 113 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8533 (tt) REVERT: A 198 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7675 (pt0) REVERT: A 704 LEU cc_start: 0.8511 (tm) cc_final: 0.8291 (tm) REVERT: A 728 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8276 (mt-10) REVERT: A 923 ASP cc_start: 0.8695 (t70) cc_final: 0.8353 (t70) REVERT: B 10 GLU cc_start: 0.8242 (tp30) cc_final: 0.7823 (tp30) REVERT: B 113 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8534 (tt) REVERT: B 198 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7693 (pt0) REVERT: B 704 LEU cc_start: 0.8510 (tm) cc_final: 0.8299 (tm) REVERT: B 728 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8282 (mt-10) REVERT: B 756 ASN cc_start: 0.7972 (m-40) cc_final: 0.7628 (m110) REVERT: B 923 ASP cc_start: 0.8686 (t70) cc_final: 0.8346 (t70) REVERT: C 10 GLU cc_start: 0.8225 (tp30) cc_final: 0.7804 (tp30) REVERT: C 113 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8544 (tt) REVERT: C 198 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7694 (pt0) REVERT: C 704 LEU cc_start: 0.8513 (tm) cc_final: 0.8304 (tm) REVERT: C 728 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8287 (mt-10) REVERT: C 923 ASP cc_start: 0.8684 (t70) cc_final: 0.8419 (t70) REVERT: D 10 GLU cc_start: 0.8246 (tp30) cc_final: 0.7828 (tp30) REVERT: D 113 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8539 (tt) REVERT: D 198 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7663 (pt0) REVERT: D 704 LEU cc_start: 0.8517 (tm) cc_final: 0.8306 (tm) REVERT: D 728 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8289 (mt-10) REVERT: D 923 ASP cc_start: 0.8676 (t70) cc_final: 0.8331 (t70) outliers start: 63 outliers final: 44 residues processed: 411 average time/residue: 0.6996 time to fit residues: 342.1430 Evaluate side-chains 406 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 354 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 947 SER Chi-restraints excluded: chain B residue 982 MET Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 548 ASP Chi-restraints excluded: chain C residue 640 GLN Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 982 MET Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 689 VAL Chi-restraints excluded: chain D residue 787 THR Chi-restraints excluded: chain D residue 947 SER Chi-restraints excluded: chain D residue 982 MET Chi-restraints excluded: chain D residue 1005 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 340 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 401 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 179 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 chunk 262 optimal weight: 6.9990 chunk 290 optimal weight: 5.9990 chunk 355 optimal weight: 6.9990 chunk 284 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.114049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.096196 restraints weight = 43033.927| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.86 r_work: 0.2925 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 33380 Z= 0.345 Angle : 0.744 7.799 45432 Z= 0.400 Chirality : 0.053 0.230 4888 Planarity : 0.006 0.049 6020 Dihedral : 5.598 27.909 4532 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.36 % Favored : 92.59 % Rotamer: Outliers : 1.98 % Allowed : 16.07 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.13), residues: 4144 helix: 1.53 (0.15), residues: 1224 sheet: -0.21 (0.15), residues: 1120 loop : -2.11 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 17 TYR 0.031 0.003 TYR B 87 PHE 0.028 0.003 PHE C 652 TRP 0.020 0.003 TRP D 282 HIS 0.009 0.001 HIS A 597 Details of bonding type rmsd covalent geometry : bond 0.00829 (33372) covalent geometry : angle 0.74355 (45432) hydrogen bonds : bond 0.06962 ( 1435) hydrogen bonds : angle 4.56267 ( 4026) metal coordination : bond 0.00147 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 363 time to evaluate : 1.298 Fit side-chains REVERT: A 10 GLU cc_start: 0.8270 (tp30) cc_final: 0.7831 (tp30) REVERT: A 113 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8543 (tt) REVERT: A 198 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7805 (pt0) REVERT: A 208 ASP cc_start: 0.8713 (t0) cc_final: 0.8398 (t0) REVERT: A 728 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8333 (mt-10) REVERT: A 756 ASN cc_start: 0.7815 (m-40) cc_final: 0.7391 (m110) REVERT: A 923 ASP cc_start: 0.8845 (t70) cc_final: 0.8498 (t70) REVERT: A 982 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8254 (tpp) REVERT: B 10 GLU cc_start: 0.8273 (tp30) cc_final: 0.7836 (tp30) REVERT: B 113 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8545 (tt) REVERT: B 198 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7808 (pt0) REVERT: B 208 ASP cc_start: 0.8706 (t0) cc_final: 0.8390 (t0) REVERT: B 640 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7586 (mt0) REVERT: B 756 ASN cc_start: 0.8137 (m-40) cc_final: 0.7760 (m110) REVERT: B 923 ASP cc_start: 0.8845 (t70) cc_final: 0.8496 (t70) REVERT: B 982 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8247 (tpp) REVERT: C 10 GLU cc_start: 0.8270 (tp30) cc_final: 0.7830 (tp30) REVERT: C 113 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8550 (tt) REVERT: C 198 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7808 (pt0) REVERT: C 208 ASP cc_start: 0.8715 (t0) cc_final: 0.8400 (t0) REVERT: C 728 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8324 (mt-10) REVERT: C 756 ASN cc_start: 0.7766 (m110) cc_final: 0.7425 (m110) REVERT: C 923 ASP cc_start: 0.8824 (t70) cc_final: 0.8515 (t70) REVERT: C 982 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8258 (tpp) REVERT: D 10 GLU cc_start: 0.8273 (tp30) cc_final: 0.7836 (tp30) REVERT: D 113 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8538 (tt) REVERT: D 198 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7790 (pt0) REVERT: D 208 ASP cc_start: 0.8705 (t0) cc_final: 0.8391 (t0) REVERT: D 640 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7590 (mt0) REVERT: D 728 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8330 (mt-10) REVERT: D 756 ASN cc_start: 0.7776 (m110) cc_final: 0.7434 (m110) REVERT: D 923 ASP cc_start: 0.8830 (t70) cc_final: 0.8483 (t70) REVERT: D 982 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8243 (tpp) outliers start: 67 outliers final: 41 residues processed: 408 average time/residue: 0.7219 time to fit residues: 348.2449 Evaluate side-chains 416 residues out of total 3392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 361 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 640 GLN Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 844 THR Chi-restraints excluded: chain B residue 947 SER Chi-restraints excluded: chain B residue 982 MET Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 548 ASP Chi-restraints excluded: chain C residue 640 GLN Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 844 THR Chi-restraints excluded: chain C residue 982 MET Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 640 GLN Chi-restraints excluded: chain D residue 689 VAL Chi-restraints excluded: chain D residue 787 THR Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 947 SER Chi-restraints excluded: chain D residue 982 MET Chi-restraints excluded: chain D residue 1005 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 99 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 257 optimal weight: 0.9980 chunk 273 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 402 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 277 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS B 109 HIS C 109 HIS D 109 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.120428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.102537 restraints weight = 42237.900| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.88 r_work: 0.3014 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33380 Z= 0.127 Angle : 0.573 7.039 45432 Z= 0.308 Chirality : 0.044 0.221 4888 Planarity : 0.004 0.037 6020 Dihedral : 5.007 26.583 4532 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.74 % Allowed : 16.24 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.13), residues: 4144 helix: 2.00 (0.15), residues: 1212 sheet: -0.10 (0.15), residues: 1100 loop : -1.89 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 635 TYR 0.016 0.001 TYR B 87 PHE 0.019 0.001 PHE A 847 TRP 0.015 0.001 TRP B 72 HIS 0.008 0.001 HIS D 597 Details of bonding type rmsd covalent geometry : bond 0.00285 (33372) covalent geometry : angle 0.57290 (45432) hydrogen bonds : bond 0.04373 ( 1435) hydrogen bonds : angle 4.31720 ( 4026) metal coordination : bond 0.00185 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9960.54 seconds wall clock time: 170 minutes 17.46 seconds (10217.46 seconds total)