Starting phenix.real_space_refine on Sat Feb 7 15:56:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hpm_52334/02_2026/9hpm_52334.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hpm_52334/02_2026/9hpm_52334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hpm_52334/02_2026/9hpm_52334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hpm_52334/02_2026/9hpm_52334.map" model { file = "/net/cci-nas-00/data/ceres_data/9hpm_52334/02_2026/9hpm_52334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hpm_52334/02_2026/9hpm_52334.cif" } resolution = 2.2 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 19944 2.51 5 N 5600 2.21 5 O 8157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33845 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7876 Classifications: {'peptide': 982} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 59, 'TRANS': 922} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 7876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7876 Classifications: {'peptide': 982} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 59, 'TRANS': 922} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 7876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7876 Classifications: {'peptide': 982} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 59, 'TRANS': 922} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 7876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7876 Classifications: {'peptide': 982} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 59, 'TRANS': 922} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 599 Classifications: {'water': 599} Link IDs: {None: 598} Chain: "B" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 592 Classifications: {'water': 592} Link IDs: {None: 591} Chain: "C" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 571 Classifications: {'water': 571} Link IDs: {None: 570} Chain: "D" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 579 Classifications: {'water': 579} Link IDs: {None: 578} Time building chain proxies: 7.73, per 1000 atoms: 0.23 Number of scatterers: 33845 At special positions: 0 Unit cell: (153.3, 193.9, 105.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 8157 8.00 N 5600 7.00 C 19944 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: 2.77 Conformation dependent library (CDL) restraints added in 1.5 seconds 7808 Ramachandran restraints generated. 3904 Oldfield, 0 Emsley, 3904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7312 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 48 sheets defined 18.7% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 Processing helix chain 'A' and resid 12 through 13 No H-bonds generated for 'chain 'A' and resid 12 through 13' Processing helix chain 'A' and resid 14 through 18 removed outlier: 3.506A pdb=" N ASN A 18 " --> pdb=" O ASP A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 130 through 136 removed outlier: 3.914A pdb=" N LEU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 196 Processing helix chain 'A' and resid 368 through 382 Processing helix chain 'A' and resid 395 through 406 removed outlier: 4.016A pdb=" N TYR A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 448 removed outlier: 3.612A pdb=" N ARG A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.599A pdb=" N ASP A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 525 removed outlier: 4.020A pdb=" N SER A 525 " --> pdb=" O LYS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.766A pdb=" N TYR A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 606 through 607 No H-bonds generated for 'chain 'A' and resid 606 through 607' Processing helix chain 'A' and resid 614 through 624 removed outlier: 4.185A pdb=" N THR A 618 " --> pdb=" O HIS A 614 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU A 619 " --> pdb=" O PRO A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 805 through 814 Processing helix chain 'A' and resid 923 through 926 Processing helix chain 'A' and resid 963 through 970 Processing helix chain 'A' and resid 972 through 976 Processing helix chain 'A' and resid 1004 through 1008 Processing helix chain 'B' and resid 6 through 11 Processing helix chain 'B' and resid 12 through 13 No H-bonds generated for 'chain 'B' and resid 12 through 13' Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.508A pdb=" N ASN B 18 " --> pdb=" O ASP B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 130 through 136 removed outlier: 3.931A pdb=" N LEU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 196 Processing helix chain 'B' and resid 368 through 382 Processing helix chain 'B' and resid 395 through 406 removed outlier: 4.016A pdb=" N TYR B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 448 removed outlier: 3.613A pdb=" N ARG B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 479 removed outlier: 3.599A pdb=" N ASP B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 525 removed outlier: 4.020A pdb=" N SER B 525 " --> pdb=" O LYS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 559 removed outlier: 3.766A pdb=" N TYR B 552 " --> pdb=" O GLY B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 606 through 607 No H-bonds generated for 'chain 'B' and resid 606 through 607' Processing helix chain 'B' and resid 614 through 624 removed outlier: 4.185A pdb=" N THR B 618 " --> pdb=" O HIS B 614 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU B 619 " --> pdb=" O PRO B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 Processing helix chain 'B' and resid 805 through 814 Processing helix chain 'B' and resid 923 through 926 Processing helix chain 'B' and resid 963 through 970 Processing helix chain 'B' and resid 972 through 976 Processing helix chain 'B' and resid 1004 through 1008 Processing helix chain 'C' and resid 6 through 11 Processing helix chain 'C' and resid 12 through 13 No H-bonds generated for 'chain 'C' and resid 12 through 13' Processing helix chain 'C' and resid 14 through 18 removed outlier: 3.505A pdb=" N ASN C 18 " --> pdb=" O ASP C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 Processing helix chain 'C' and resid 65 through 69 Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 89 through 94 Processing helix chain 'C' and resid 130 through 136 removed outlier: 3.957A pdb=" N LEU C 134 " --> pdb=" O ASP C 130 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 196 Processing helix chain 'C' and resid 368 through 382 Processing helix chain 'C' and resid 395 through 406 removed outlier: 4.015A pdb=" N TYR C 399 " --> pdb=" O HIS C 395 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 432 through 448 removed outlier: 3.613A pdb=" N ARG C 439 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 479 removed outlier: 3.599A pdb=" N ASP C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 525 removed outlier: 4.020A pdb=" N SER C 525 " --> pdb=" O LYS C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 559 removed outlier: 3.767A pdb=" N TYR C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 606 through 607 No H-bonds generated for 'chain 'C' and resid 606 through 607' Processing helix chain 'C' and resid 614 through 624 removed outlier: 4.185A pdb=" N THR C 618 " --> pdb=" O HIS C 614 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU C 619 " --> pdb=" O PRO C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 794 Processing helix chain 'C' and resid 805 through 814 Processing helix chain 'C' and resid 923 through 926 Processing helix chain 'C' and resid 963 through 970 Processing helix chain 'C' and resid 972 through 976 Processing helix chain 'C' and resid 1004 through 1008 Processing helix chain 'D' and resid 6 through 11 Processing helix chain 'D' and resid 12 through 13 No H-bonds generated for 'chain 'D' and resid 12 through 13' Processing helix chain 'D' and resid 14 through 18 removed outlier: 3.504A pdb=" N ASN D 18 " --> pdb=" O ASP D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 44 Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 70 through 75 Processing helix chain 'D' and resid 89 through 94 Processing helix chain 'D' and resid 130 through 136 removed outlier: 3.933A pdb=" N LEU D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 196 Processing helix chain 'D' and resid 368 through 382 Processing helix chain 'D' and resid 395 through 406 removed outlier: 4.016A pdb=" N TYR D 399 " --> pdb=" O HIS D 395 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 432 through 448 removed outlier: 3.613A pdb=" N ARG D 439 " --> pdb=" O ALA D 435 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET D 443 " --> pdb=" O ARG D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 479 removed outlier: 3.599A pdb=" N ASP D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 525 removed outlier: 4.020A pdb=" N SER D 525 " --> pdb=" O LYS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.767A pdb=" N TYR D 552 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 571 No H-bonds generated for 'chain 'D' and resid 569 through 571' Processing helix chain 'D' and resid 606 through 607 No H-bonds generated for 'chain 'D' and resid 606 through 607' Processing helix chain 'D' and resid 614 through 624 removed outlier: 4.185A pdb=" N THR D 618 " --> pdb=" O HIS D 614 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU D 619 " --> pdb=" O PRO D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 794 Processing helix chain 'D' and resid 805 through 814 Processing helix chain 'D' and resid 923 through 926 Processing helix chain 'D' and resid 963 through 970 Processing helix chain 'D' and resid 972 through 976 Processing helix chain 'D' and resid 1004 through 1008 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 53 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 85 removed outlier: 8.432A pdb=" N GLU A 57 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N THR A 126 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY A 180 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 149 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N PHE A 150 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N TYR A 161 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU A 152 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 199 Processing sheet with id=AA4, first strand: chain 'A' and resid 221 through 231 removed outlier: 5.470A pdb=" N ILE A 222 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N CYS A 247 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 273 removed outlier: 5.558A pdb=" N GLN A 266 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN A 262 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 268 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR A 317 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU A 322 " --> pdb=" O THR A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 335 through 338 Processing sheet with id=AA7, first strand: chain 'A' and resid 484 through 485 removed outlier: 8.042A pdb=" N GLN A 485 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TRP A 456 " --> pdb=" O GLN A 485 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL A 409 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N SER A 457 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP A 411 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU A 412 " --> pdb=" O CYS A 389 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ARG A 352 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ARG A 388 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL A 354 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU A 533 " --> pdb=" O GLY A 564 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N PHE A 566 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU A 535 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 627 through 632 Processing sheet with id=AA9, first strand: chain 'A' and resid 661 through 669 removed outlier: 5.844A pdb=" N LEU A 658 " --> pdb=" O PRO A 662 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY A 692 " --> pdb=" O GLU A 724 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU A 724 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU A 694 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA A 716 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLN A 702 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE A 714 " --> pdb=" O GLN A 702 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 739 through 742 removed outlier: 6.112A pdb=" N ASN A 759 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU A 765 " --> pdb=" O ASN A 759 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 776 through 783 removed outlier: 5.356A pdb=" N GLN A 887 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 11.735A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP A 954 " --> pdb=" O GLN A1017 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLN A1017 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 10.551A pdb=" N GLN A 956 " --> pdb=" O HIS A1015 " (cutoff:3.500A) removed outlier: 13.592A pdb=" N HIS A1015 " --> pdb=" O GLN A 956 " (cutoff:3.500A) removed outlier: 20.604A pdb=" N ASN A 958 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 23.488A pdb=" N ARG A1013 " --> pdb=" O ASN A 958 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP A 842 " --> pdb=" O LEU A 849 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE A 851 " --> pdb=" O HIS A 840 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N HIS A 840 " --> pdb=" O ILE A 851 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ARG A 853 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR A 838 " --> pdb=" O ARG A 853 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR A 855 " --> pdb=" O ILE A 836 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE A 836 " --> pdb=" O THR A 855 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ARG A 857 " --> pdb=" O VAL A 834 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL A 834 " --> pdb=" O ARG A 857 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA A 833 " --> pdb=" O THR A 829 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N THR A 829 " --> pdb=" O ALA A 833 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A 835 " --> pdb=" O ALA A 827 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA A 827 " --> pdb=" O LEU A 835 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR A 837 " --> pdb=" O CYS A 825 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N CYS A 825 " --> pdb=" O THR A 837 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA A 839 " --> pdb=" O LEU A 823 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 843 " --> pdb=" O GLU A 819 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 776 through 783 removed outlier: 5.356A pdb=" N GLN A 887 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 11.735A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG A 942 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N PHE A 955 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY A 940 " --> pdb=" O PHE A 955 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR A 941 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LEU A 900 " --> pdb=" O THR A 941 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AB5, first strand: chain 'B' and resid 82 through 85 removed outlier: 8.435A pdb=" N GLU B 57 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N THR B 126 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY B 180 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 149 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE B 150 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR B 161 " --> pdb=" O PHE B 150 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU B 152 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 198 through 199 Processing sheet with id=AB7, first strand: chain 'B' and resid 221 through 231 removed outlier: 5.470A pdb=" N ILE B 222 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N CYS B 247 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 265 through 273 removed outlier: 5.558A pdb=" N GLN B 266 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLN B 262 " --> pdb=" O GLN B 266 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 268 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR B 317 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU B 322 " --> pdb=" O THR B 317 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 335 through 338 Processing sheet with id=AC1, first strand: chain 'B' and resid 484 through 485 removed outlier: 8.044A pdb=" N GLN B 485 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TRP B 456 " --> pdb=" O GLN B 485 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B 409 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N SER B 457 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP B 411 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU B 412 " --> pdb=" O CYS B 389 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ARG B 352 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ARG B 388 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 354 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU B 533 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N PHE B 566 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU B 535 " --> pdb=" O PHE B 566 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 627 through 632 Processing sheet with id=AC3, first strand: chain 'B' and resid 661 through 669 removed outlier: 5.846A pdb=" N LEU B 658 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY B 692 " --> pdb=" O GLU B 724 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLU B 724 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU B 694 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA B 716 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLN B 702 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE B 714 " --> pdb=" O GLN B 702 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 739 through 742 removed outlier: 6.117A pdb=" N ASN B 759 " --> pdb=" O LEU B 765 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU B 765 " --> pdb=" O ASN B 759 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 776 through 783 removed outlier: 5.358A pdb=" N GLN B 887 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 11.737A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASP B 954 " --> pdb=" O GLN B1017 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLN B1017 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 10.550A pdb=" N GLN B 956 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 13.587A pdb=" N HIS B1015 " --> pdb=" O GLN B 956 " (cutoff:3.500A) removed outlier: 20.604A pdb=" N ASN B 958 " --> pdb=" O ARG B1013 " (cutoff:3.500A) removed outlier: 23.488A pdb=" N ARG B1013 " --> pdb=" O ASN B 958 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP B 842 " --> pdb=" O LEU B 849 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE B 851 " --> pdb=" O HIS B 840 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N HIS B 840 " --> pdb=" O ILE B 851 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG B 853 " --> pdb=" O THR B 838 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N THR B 838 " --> pdb=" O ARG B 853 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR B 855 " --> pdb=" O ILE B 836 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE B 836 " --> pdb=" O THR B 855 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG B 857 " --> pdb=" O VAL B 834 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL B 834 " --> pdb=" O ARG B 857 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ALA B 833 " --> pdb=" O THR B 829 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N THR B 829 " --> pdb=" O ALA B 833 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 835 " --> pdb=" O ALA B 827 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA B 827 " --> pdb=" O LEU B 835 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR B 837 " --> pdb=" O CYS B 825 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N CYS B 825 " --> pdb=" O THR B 837 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA B 839 " --> pdb=" O LEU B 823 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN B 843 " --> pdb=" O GLU B 819 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 776 through 783 removed outlier: 5.358A pdb=" N GLN B 887 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 11.737A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG B 942 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE B 955 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY B 940 " --> pdb=" O PHE B 955 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR B 941 " --> pdb=" O LEU B 900 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU B 900 " --> pdb=" O THR B 941 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 51 through 53 Processing sheet with id=AC8, first strand: chain 'C' and resid 82 through 85 removed outlier: 8.425A pdb=" N GLU C 57 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N THR C 126 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY C 180 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA C 149 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N PHE C 150 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N TYR C 161 " --> pdb=" O PHE C 150 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU C 152 " --> pdb=" O VAL C 159 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 198 through 199 Processing sheet with id=AD1, first strand: chain 'C' and resid 221 through 231 removed outlier: 5.472A pdb=" N ILE C 222 " --> pdb=" O CYS C 247 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N CYS C 247 " --> pdb=" O ILE C 222 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 265 through 273 removed outlier: 5.558A pdb=" N GLN C 266 " --> pdb=" O GLN C 262 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLN C 262 " --> pdb=" O GLN C 266 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA C 268 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR C 317 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU C 322 " --> pdb=" O THR C 317 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 335 through 338 Processing sheet with id=AD4, first strand: chain 'C' and resid 484 through 485 removed outlier: 8.047A pdb=" N GLN C 485 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N TRP C 456 " --> pdb=" O GLN C 485 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL C 409 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N SER C 457 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP C 411 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU C 412 " --> pdb=" O CYS C 389 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ARG C 352 " --> pdb=" O ALA C 386 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ARG C 388 " --> pdb=" O ARG C 352 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL C 354 " --> pdb=" O ARG C 388 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU C 533 " --> pdb=" O GLY C 564 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N PHE C 566 " --> pdb=" O LEU C 533 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU C 535 " --> pdb=" O PHE C 566 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 627 through 632 Processing sheet with id=AD6, first strand: chain 'C' and resid 661 through 669 removed outlier: 6.711A pdb=" N VAL C 656 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N SER C 665 " --> pdb=" O TRP C 654 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TRP C 654 " --> pdb=" O SER C 665 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU C 667 " --> pdb=" O LEU C 652 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU C 652 " --> pdb=" O GLU C 667 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLY C 692 " --> pdb=" O GLU C 724 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLU C 724 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU C 694 " --> pdb=" O LEU C 722 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA C 716 " --> pdb=" O VAL C 700 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLN C 702 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE C 714 " --> pdb=" O GLN C 702 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 739 through 742 removed outlier: 6.114A pdb=" N ASN C 759 " --> pdb=" O LEU C 765 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU C 765 " --> pdb=" O ASN C 759 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 776 through 783 removed outlier: 5.359A pdb=" N GLN C 887 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 11.736A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP C 954 " --> pdb=" O GLN C1017 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLN C1017 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 10.550A pdb=" N GLN C 956 " --> pdb=" O HIS C1015 " (cutoff:3.500A) removed outlier: 13.591A pdb=" N HIS C1015 " --> pdb=" O GLN C 956 " (cutoff:3.500A) removed outlier: 20.605A pdb=" N ASN C 958 " --> pdb=" O ARG C1013 " (cutoff:3.500A) removed outlier: 23.489A pdb=" N ARG C1013 " --> pdb=" O ASN C 958 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP C 842 " --> pdb=" O LEU C 849 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE C 851 " --> pdb=" O HIS C 840 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N HIS C 840 " --> pdb=" O ILE C 851 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ARG C 853 " --> pdb=" O THR C 838 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR C 838 " --> pdb=" O ARG C 853 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR C 855 " --> pdb=" O ILE C 836 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE C 836 " --> pdb=" O THR C 855 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG C 857 " --> pdb=" O VAL C 834 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL C 834 " --> pdb=" O ARG C 857 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA C 833 " --> pdb=" O THR C 829 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N THR C 829 " --> pdb=" O ALA C 833 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU C 835 " --> pdb=" O ALA C 827 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA C 827 " --> pdb=" O LEU C 835 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR C 837 " --> pdb=" O CYS C 825 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N CYS C 825 " --> pdb=" O THR C 837 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA C 839 " --> pdb=" O LEU C 823 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN C 843 " --> pdb=" O GLU C 819 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 776 through 783 removed outlier: 5.359A pdb=" N GLN C 887 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 11.736A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG C 942 " --> pdb=" O GLY C 953 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N PHE C 955 " --> pdb=" O GLY C 940 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY C 940 " --> pdb=" O PHE C 955 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR C 941 " --> pdb=" O LEU C 900 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU C 900 " --> pdb=" O THR C 941 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AE2, first strand: chain 'D' and resid 82 through 85 removed outlier: 8.426A pdb=" N GLU D 57 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N THR D 126 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY D 180 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA D 149 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE D 150 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TYR D 161 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU D 152 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 198 through 199 Processing sheet with id=AE4, first strand: chain 'D' and resid 221 through 231 removed outlier: 5.466A pdb=" N ILE D 222 " --> pdb=" O CYS D 247 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N CYS D 247 " --> pdb=" O ILE D 222 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 265 through 273 removed outlier: 5.558A pdb=" N GLN D 266 " --> pdb=" O GLN D 262 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN D 262 " --> pdb=" O GLN D 266 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 268 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR D 317 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU D 322 " --> pdb=" O THR D 317 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 335 through 338 Processing sheet with id=AE7, first strand: chain 'D' and resid 484 through 485 removed outlier: 8.044A pdb=" N GLN D 485 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TRP D 456 " --> pdb=" O GLN D 485 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL D 409 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER D 457 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP D 411 " --> pdb=" O SER D 457 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU D 412 " --> pdb=" O CYS D 389 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ARG D 352 " --> pdb=" O ALA D 386 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ARG D 388 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL D 354 " --> pdb=" O ARG D 388 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU D 533 " --> pdb=" O GLY D 564 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N PHE D 566 " --> pdb=" O LEU D 533 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU D 535 " --> pdb=" O PHE D 566 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 627 through 632 Processing sheet with id=AE9, first strand: chain 'D' and resid 661 through 669 removed outlier: 5.844A pdb=" N LEU D 658 " --> pdb=" O PRO D 662 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLY D 692 " --> pdb=" O GLU D 724 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU D 724 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU D 694 " --> pdb=" O LEU D 722 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA D 716 " --> pdb=" O VAL D 700 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLN D 702 " --> pdb=" O ILE D 714 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE D 714 " --> pdb=" O GLN D 702 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 739 through 742 removed outlier: 6.118A pdb=" N ASN D 759 " --> pdb=" O LEU D 765 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LEU D 765 " --> pdb=" O ASN D 759 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 776 through 783 removed outlier: 5.379A pdb=" N GLN D 887 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 11.738A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP D 954 " --> pdb=" O GLN D1017 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLN D1017 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 10.551A pdb=" N GLN D 956 " --> pdb=" O HIS D1015 " (cutoff:3.500A) removed outlier: 13.592A pdb=" N HIS D1015 " --> pdb=" O GLN D 956 " (cutoff:3.500A) removed outlier: 20.604A pdb=" N ASN D 958 " --> pdb=" O ARG D1013 " (cutoff:3.500A) removed outlier: 23.488A pdb=" N ARG D1013 " --> pdb=" O ASN D 958 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP D 842 " --> pdb=" O LEU D 849 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE D 851 " --> pdb=" O HIS D 840 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N HIS D 840 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG D 853 " --> pdb=" O THR D 838 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR D 838 " --> pdb=" O ARG D 853 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR D 855 " --> pdb=" O ILE D 836 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE D 836 " --> pdb=" O THR D 855 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ARG D 857 " --> pdb=" O VAL D 834 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL D 834 " --> pdb=" O ARG D 857 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA D 833 " --> pdb=" O THR D 829 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N THR D 829 " --> pdb=" O ALA D 833 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU D 835 " --> pdb=" O ALA D 827 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA D 827 " --> pdb=" O LEU D 835 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR D 837 " --> pdb=" O CYS D 825 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N CYS D 825 " --> pdb=" O THR D 837 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA D 839 " --> pdb=" O LEU D 823 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN D 843 " --> pdb=" O GLU D 819 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 776 through 783 removed outlier: 5.379A pdb=" N GLN D 887 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 11.738A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG D 942 " --> pdb=" O GLY D 953 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N PHE D 955 " --> pdb=" O GLY D 940 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY D 940 " --> pdb=" O PHE D 955 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR D 941 " --> pdb=" O LEU D 900 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU D 900 " --> pdb=" O THR D 941 " (cutoff:3.500A) 1193 hydrogen bonds defined for protein. 3144 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: 11.36 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10611 1.34 - 1.46: 7719 1.46 - 1.58: 13866 1.58 - 1.70: 0 1.70 - 1.81: 228 Bond restraints: 32424 Sorted by residual: bond pdb=" C LEU A 433 " pdb=" N PRO A 434 " ideal model delta sigma weight residual 1.335 1.355 -0.019 1.36e-02 5.41e+03 2.03e+00 bond pdb=" C LEU B 433 " pdb=" N PRO B 434 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.36e-02 5.41e+03 1.86e+00 bond pdb=" C LEU D 433 " pdb=" N PRO D 434 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.36e-02 5.41e+03 1.86e+00 bond pdb=" C LEU C 433 " pdb=" N PRO C 434 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.36e-02 5.41e+03 1.86e+00 bond pdb=" C VAL C 86 " pdb=" N PRO C 87 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.23e+00 ... (remaining 32419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 43219 1.41 - 2.82: 780 2.82 - 4.24: 184 4.24 - 5.65: 36 5.65 - 7.06: 5 Bond angle restraints: 44224 Sorted by residual: angle pdb=" N ASP D 569 " pdb=" CA ASP D 569 " pdb=" C ASP D 569 " ideal model delta sigma weight residual 110.91 114.40 -3.49 1.17e+00 7.31e-01 8.89e+00 angle pdb=" N ASP A 569 " pdb=" CA ASP A 569 " pdb=" C ASP A 569 " ideal model delta sigma weight residual 110.91 114.40 -3.49 1.17e+00 7.31e-01 8.88e+00 angle pdb=" N ASP C 569 " pdb=" CA ASP C 569 " pdb=" C ASP C 569 " ideal model delta sigma weight residual 110.91 114.39 -3.48 1.17e+00 7.31e-01 8.83e+00 angle pdb=" N ASP B 569 " pdb=" CA ASP B 569 " pdb=" C ASP B 569 " ideal model delta sigma weight residual 110.91 114.36 -3.45 1.17e+00 7.31e-01 8.71e+00 angle pdb=" C PRO C 422 " pdb=" N MET C 423 " pdb=" CA MET C 423 " ideal model delta sigma weight residual 121.54 126.37 -4.83 1.91e+00 2.74e-01 6.38e+00 ... (remaining 44219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 16689 17.04 - 34.07: 1639 34.07 - 51.11: 406 51.11 - 68.14: 163 68.14 - 85.18: 95 Dihedral angle restraints: 18992 sinusoidal: 7652 harmonic: 11340 Sorted by residual: dihedral pdb=" CA ASP A 569 " pdb=" C ASP A 569 " pdb=" N TRP A 570 " pdb=" CA TRP A 570 " ideal model delta harmonic sigma weight residual 180.00 160.52 19.48 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ASP B 569 " pdb=" C ASP B 569 " pdb=" N TRP B 570 " pdb=" CA TRP B 570 " ideal model delta harmonic sigma weight residual 180.00 160.53 19.47 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ASP C 569 " pdb=" C ASP C 569 " pdb=" N TRP C 570 " pdb=" CA TRP C 570 " ideal model delta harmonic sigma weight residual 180.00 160.56 19.44 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 18989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2896 0.032 - 0.063: 1164 0.063 - 0.095: 296 0.095 - 0.126: 269 0.126 - 0.158: 19 Chirality restraints: 4644 Sorted by residual: chirality pdb=" CA VAL C 86 " pdb=" N VAL C 86 " pdb=" C VAL C 86 " pdb=" CB VAL C 86 " both_signs ideal model delta sigma weight residual False 2.44 2.28 0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" CA VAL D 86 " pdb=" N VAL D 86 " pdb=" C VAL D 86 " pdb=" CB VAL D 86 " both_signs ideal model delta sigma weight residual False 2.44 2.28 0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA VAL A 86 " pdb=" N VAL A 86 " pdb=" C VAL A 86 " pdb=" CB VAL A 86 " both_signs ideal model delta sigma weight residual False 2.44 2.28 0.16 2.00e-01 2.50e+01 6.19e-01 ... (remaining 4641 not shown) Planarity restraints: 5820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 421 " -0.034 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO D 422 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 422 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 422 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 421 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO C 422 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 422 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 422 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 421 " 0.033 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO A 422 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 422 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 422 " 0.028 5.00e-02 4.00e+02 ... (remaining 5817 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 4505 2.75 - 3.29: 31936 3.29 - 3.83: 64256 3.83 - 4.36: 81334 4.36 - 4.90: 129290 Nonbonded interactions: 311321 Sorted by model distance: nonbonded pdb=" OE1 GLU C 461 " pdb=" O HOH C1101 " model vdw 2.216 3.040 nonbonded pdb=" OE1 GLU A 461 " pdb=" O HOH A1101 " model vdw 2.217 3.040 nonbonded pdb=" OE1 GLU D 461 " pdb=" O HOH D1101 " model vdw 2.217 3.040 nonbonded pdb=" OE1 GLU B 461 " pdb=" O HOH B1101 " model vdw 2.218 3.040 nonbonded pdb=" OD1 ASP D 828 " pdb=" O HOH D1102 " model vdw 2.219 3.040 ... (remaining 311316 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: 6.040 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: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 36.190 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.090 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:8.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 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 : 0.002 0.029 32424 Z= 0.113 Angle : 0.518 7.058 44224 Z= 0.277 Chirality : 0.043 0.158 4644 Planarity : 0.004 0.051 5820 Dihedral : 16.518 85.177 11680 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.82 % Allowed : 14.14 % Favored : 84.03 % 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: 0.28 (0.13), residues: 3904 helix: -0.49 (0.23), residues: 500 sheet: 1.03 (0.14), residues: 1284 loop : -0.10 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 59 TYR 0.011 0.001 TYR D 486 PHE 0.008 0.001 PHE D 274 TRP 0.027 0.001 TRP A 553 HIS 0.007 0.001 HIS D 974 Details of bonding type rmsd covalent geometry : bond 0.00239 (32424) covalent geometry : angle 0.51772 (44224) hydrogen bonds : bond 0.19450 ( 1125) hydrogen bonds : angle 7.29652 ( 3144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7808 Ramachandran restraints generated. 3904 Oldfield, 0 Emsley, 3904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7808 Ramachandran restraints generated. 3904 Oldfield, 0 Emsley, 3904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 402 time to evaluate : 1.354 Fit side-chains REVERT: A 135 GLN cc_start: 0.7690 (mm-40) cc_final: 0.7420 (mm110) REVERT: A 768 MET cc_start: 0.8074 (ttt) cc_final: 0.7739 (ttm) REVERT: B 551 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8920 (mtmt) REVERT: C 423 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7805 (ttp) REVERT: C 551 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8920 (mtmt) REVERT: C 768 MET cc_start: 0.8066 (ttt) cc_final: 0.7727 (ttm) REVERT: D 423 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7754 (ttp) REVERT: D 551 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8934 (mtmt) REVERT: D 768 MET cc_start: 0.8054 (ttt) cc_final: 0.7747 (ttm) outliers start: 61 outliers final: 49 residues processed: 458 average time/residue: 0.8684 time to fit residues: 462.0082 Evaluate side-chains 443 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 389 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 875 ASP Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 551 LYS Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 797 GLU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 875 ASP Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 LYS Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 797 GLU Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain C residue 875 ASP Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 423 MET Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 551 LYS Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 797 GLU Chi-restraints excluded: chain D residue 867 THR Chi-restraints excluded: chain D residue 875 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 HIS A 653 HIS A 761 GLN A 972 HIS B 614 HIS B 653 HIS B 761 GLN B 972 HIS C 614 HIS C 653 HIS C 761 GLN C 972 HIS D 614 HIS D 653 HIS D 761 GLN D 885 ASN D 972 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.129862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.099347 restraints weight = 35935.875| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.54 r_work: 0.3076 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 32424 Z= 0.350 Angle : 0.760 8.636 44224 Z= 0.410 Chirality : 0.055 0.243 4644 Planarity : 0.007 0.114 5820 Dihedral : 7.519 67.944 4383 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.71 % Favored : 96.18 % Rotamer: Outliers : 3.11 % Allowed : 11.72 % Favored : 85.17 % 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: 0.13 (0.13), residues: 3904 helix: -0.21 (0.22), residues: 508 sheet: 1.03 (0.14), residues: 1264 loop : -0.38 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 557 TYR 0.020 0.003 TYR B 906 PHE 0.020 0.003 PHE A 274 TRP 0.043 0.003 TRP A 553 HIS 0.008 0.002 HIS C 226 Details of bonding type rmsd covalent geometry : bond 0.00795 (32424) covalent geometry : angle 0.75984 (44224) hydrogen bonds : bond 0.06547 ( 1125) hydrogen bonds : angle 5.67779 ( 3144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7808 Ramachandran restraints generated. 3904 Oldfield, 0 Emsley, 3904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7808 Ramachandran restraints generated. 3904 Oldfield, 0 Emsley, 3904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 392 time to evaluate : 1.315 Fit side-chains REVERT: A 202 MET cc_start: 0.6982 (OUTLIER) cc_final: 0.6541 (ptt) REVERT: B 202 MET cc_start: 0.6951 (OUTLIER) cc_final: 0.6581 (ptt) REVERT: C 59 ARG cc_start: 0.8448 (mmm-85) cc_final: 0.8201 (mmm-85) REVERT: C 202 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6556 (ptt) REVERT: D 202 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.6403 (ptt) outliers start: 104 outliers final: 70 residues processed: 457 average time/residue: 0.8619 time to fit residues: 458.5795 Evaluate side-chains 449 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 375 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 817 GLN Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 817 GLN Chi-restraints excluded: chain B residue 825 CYS Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 859 ASP Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 817 GLN Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 904 GLU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 741 THR Chi-restraints excluded: chain D residue 768 MET Chi-restraints excluded: chain D residue 817 GLN Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain D residue 859 ASP Chi-restraints excluded: chain D residue 861 SER Chi-restraints excluded: chain D residue 904 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 386 optimal weight: 4.9990 chunk 327 optimal weight: 7.9990 chunk 329 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 353 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 246 optimal weight: 0.3980 chunk 87 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 761 GLN A 972 HIS B 135 GLN B 761 GLN B 972 HIS C 135 GLN C 761 GLN C 972 HIS D 135 GLN D 761 GLN D 783 GLN D 885 ASN D 972 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.135255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.105373 restraints weight = 35799.074| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.54 r_work: 0.3159 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 32424 Z= 0.115 Angle : 0.534 6.959 44224 Z= 0.286 Chirality : 0.045 0.163 4644 Planarity : 0.004 0.051 5820 Dihedral : 5.991 57.143 4325 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.58 % Allowed : 13.22 % Favored : 85.20 % 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: 0.36 (0.13), residues: 3904 helix: 0.41 (0.23), residues: 508 sheet: 1.08 (0.14), residues: 1288 loop : -0.29 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 59 TYR 0.011 0.001 TYR D 196 PHE 0.012 0.001 PHE D 549 TRP 0.037 0.001 TRP D 553 HIS 0.006 0.001 HIS C 974 Details of bonding type rmsd covalent geometry : bond 0.00240 (32424) covalent geometry : angle 0.53389 (44224) hydrogen bonds : bond 0.04192 ( 1125) hydrogen bonds : angle 5.12470 ( 3144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7808 Ramachandran restraints generated. 3904 Oldfield, 0 Emsley, 3904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7808 Ramachandran restraints generated. 3904 Oldfield, 0 Emsley, 3904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 416 time to evaluate : 1.450 Fit side-chains REVERT: A 67 GLU cc_start: 0.8052 (mp0) cc_final: 0.7687 (mp0) REVERT: A 135 GLN cc_start: 0.7626 (mm-40) cc_final: 0.7073 (mt0) REVERT: A 859 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7411 (p0) REVERT: B 67 GLU cc_start: 0.8020 (mp0) cc_final: 0.7667 (mp0) REVERT: B 135 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7139 (mt0) REVERT: B 721 ARG cc_start: 0.8356 (mtp85) cc_final: 0.8131 (mtp85) REVERT: B 859 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7384 (p0) REVERT: C 59 ARG cc_start: 0.8436 (mmm-85) cc_final: 0.8172 (mmm-85) REVERT: C 67 GLU cc_start: 0.8019 (mp0) cc_final: 0.7661 (mp0) REVERT: C 135 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7132 (mt0) REVERT: C 859 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7397 (p0) REVERT: D 67 GLU cc_start: 0.8057 (mp0) cc_final: 0.7686 (mp0) REVERT: D 135 GLN cc_start: 0.7685 (mm-40) cc_final: 0.7122 (mt0) REVERT: D 423 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7666 (tpp) REVERT: D 859 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7406 (p0) outliers start: 53 outliers final: 29 residues processed: 442 average time/residue: 0.8396 time to fit residues: 430.5794 Evaluate side-chains 433 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 399 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 817 GLN Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 817 GLN Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 859 ASP Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 817 GLN Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 423 MET Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 768 MET Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 817 GLN Chi-restraints excluded: chain D residue 859 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 163 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 123 optimal weight: 0.0070 chunk 127 optimal weight: 0.9980 chunk 350 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 140 optimal weight: 0.9980 chunk 366 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 761 GLN A 972 HIS B 761 GLN B 775 GLN B 972 HIS B1022 GLN C 761 GLN C 783 GLN C 885 ASN C 972 HIS D 761 GLN D 885 ASN D 972 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.136925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.107883 restraints weight = 35931.262| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.52 r_work: 0.3197 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 32424 Z= 0.096 Angle : 0.499 7.030 44224 Z= 0.265 Chirality : 0.044 0.163 4644 Planarity : 0.004 0.043 5820 Dihedral : 4.971 51.433 4297 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.82 % Allowed : 13.76 % Favored : 84.42 % 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: 0.47 (0.13), residues: 3904 helix: 0.72 (0.22), residues: 536 sheet: 1.07 (0.14), residues: 1288 loop : -0.24 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 442 TYR 0.009 0.001 TYR A 486 PHE 0.011 0.001 PHE A 758 TRP 0.033 0.001 TRP D 553 HIS 0.007 0.001 HIS B 974 Details of bonding type rmsd covalent geometry : bond 0.00201 (32424) covalent geometry : angle 0.49916 (44224) hydrogen bonds : bond 0.03596 ( 1125) hydrogen bonds : angle 4.79122 ( 3144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7808 Ramachandran restraints generated. 3904 Oldfield, 0 Emsley, 3904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7808 Ramachandran restraints generated. 3904 Oldfield, 0 Emsley, 3904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 426 time to evaluate : 1.279 Fit side-chains REVERT: A 59 ARG cc_start: 0.8515 (mmm-85) cc_final: 0.8314 (mmm-85) REVERT: A 67 GLU cc_start: 0.8056 (mp0) cc_final: 0.7692 (mp0) REVERT: A 135 GLN cc_start: 0.7527 (mm-40) cc_final: 0.7236 (mt0) REVERT: A 423 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7732 (tpp) REVERT: A 817 GLN cc_start: 0.7433 (OUTLIER) cc_final: 0.7208 (mm-40) REVERT: A 859 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7414 (p0) REVERT: A 863 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7255 (mt0) REVERT: B 59 ARG cc_start: 0.8534 (mmm-85) cc_final: 0.8319 (mmm-85) REVERT: B 67 GLU cc_start: 0.8030 (mp0) cc_final: 0.7677 (mp0) REVERT: B 423 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7746 (tpp) REVERT: B 859 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7407 (p0) REVERT: B 863 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7243 (mt0) REVERT: C 59 ARG cc_start: 0.8415 (mmm-85) cc_final: 0.8160 (mmm-85) REVERT: C 67 GLU cc_start: 0.8035 (mp0) cc_final: 0.7683 (mp0) REVERT: C 135 GLN cc_start: 0.7553 (mm-40) cc_final: 0.7200 (mt0) REVERT: C 423 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7751 (tpp) REVERT: C 859 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7403 (p0) REVERT: C 863 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7260 (mt0) REVERT: D 59 ARG cc_start: 0.8508 (mmm-85) cc_final: 0.8307 (mmm-85) REVERT: D 67 GLU cc_start: 0.8054 (mp0) cc_final: 0.7686 (mp0) REVERT: D 135 GLN cc_start: 0.7592 (mm-40) cc_final: 0.7202 (mt0) REVERT: D 423 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7760 (tpp) REVERT: D 859 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7412 (p0) REVERT: D 863 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7248 (mt0) outliers start: 61 outliers final: 22 residues processed: 456 average time/residue: 0.8530 time to fit residues: 451.1676 Evaluate side-chains 441 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 406 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 817 GLN Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 859 ASP Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain C residue 867 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 423 MET Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 768 MET Chi-restraints excluded: chain D residue 859 ASP Chi-restraints excluded: chain D residue 863 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 310 optimal weight: 4.9990 chunk 128 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 285 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 322 optimal weight: 10.0000 chunk 228 optimal weight: 0.6980 chunk 190 optimal weight: 10.0000 chunk 351 optimal weight: 7.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 761 GLN ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 972 HIS ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN B 357 HIS B 761 GLN B 972 HIS C 357 HIS C 761 GLN C 972 HIS D 357 HIS D 761 GLN ** D 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 972 HIS ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.133330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.102986 restraints weight = 35886.994| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.55 r_work: 0.3133 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 32424 Z= 0.169 Angle : 0.576 7.592 44224 Z= 0.307 Chirality : 0.046 0.175 4644 Planarity : 0.005 0.057 5820 Dihedral : 5.397 54.563 4296 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.15 % Allowed : 13.55 % Favored : 84.30 % 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: 0.46 (0.13), residues: 3904 helix: 0.57 (0.22), residues: 532 sheet: 1.10 (0.14), residues: 1316 loop : -0.25 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 557 TYR 0.014 0.002 TYR D 906 PHE 0.013 0.002 PHE A 274 TRP 0.030 0.002 TRP B 553 HIS 0.008 0.001 HIS B 974 Details of bonding type rmsd covalent geometry : bond 0.00372 (32424) covalent geometry : angle 0.57562 (44224) hydrogen bonds : bond 0.04518 ( 1125) hydrogen bonds : angle 5.02507 ( 3144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7808 Ramachandran restraints generated. 3904 Oldfield, 0 Emsley, 3904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7808 Ramachandran restraints generated. 3904 Oldfield, 0 Emsley, 3904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 413 time to evaluate : 1.364 Fit side-chains REVERT: A 59 ARG cc_start: 0.8519 (mmm-85) cc_final: 0.8256 (mmm-85) REVERT: A 67 GLU cc_start: 0.8041 (mp0) cc_final: 0.7664 (mp0) REVERT: A 135 GLN cc_start: 0.7537 (mm-40) cc_final: 0.7168 (mt0) REVERT: A 423 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7859 (ttp) REVERT: A 859 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7421 (p0) REVERT: A 864 MET cc_start: 0.9037 (ttt) cc_final: 0.8683 (ttt) REVERT: B 59 ARG cc_start: 0.8535 (mmm-85) cc_final: 0.8272 (mmm-85) REVERT: B 67 GLU cc_start: 0.8020 (mp0) cc_final: 0.7652 (mp0) REVERT: B 135 GLN cc_start: 0.7528 (mm-40) cc_final: 0.7036 (mt0) REVERT: B 423 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7856 (ttp) REVERT: B 859 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7422 (p0) REVERT: C 59 ARG cc_start: 0.8396 (mmm-85) cc_final: 0.8127 (mmm-85) REVERT: C 67 GLU cc_start: 0.8024 (mp0) cc_final: 0.7638 (mp0) REVERT: C 135 GLN cc_start: 0.7572 (mm-40) cc_final: 0.7188 (mt0) REVERT: C 423 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7843 (ttp) REVERT: C 859 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7452 (p0) REVERT: C 864 MET cc_start: 0.9028 (ttt) cc_final: 0.8671 (ttt) REVERT: D 59 ARG cc_start: 0.8520 (mmm-85) cc_final: 0.8256 (mmm-85) REVERT: D 67 GLU cc_start: 0.8051 (mp0) cc_final: 0.7660 (mp0) REVERT: D 205 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.7062 (mmm) REVERT: D 423 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7819 (ttp) REVERT: D 859 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7426 (p0) REVERT: D 864 MET cc_start: 0.9035 (ttt) cc_final: 0.8680 (ttt) outliers start: 72 outliers final: 36 residues processed: 453 average time/residue: 0.8539 time to fit residues: 450.2617 Evaluate side-chains 445 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 400 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 817 GLN Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 817 GLN Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 859 ASP Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 817 GLN Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 423 MET Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 768 MET Chi-restraints excluded: chain D residue 859 ASP Chi-restraints excluded: chain D residue 861 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 327 optimal weight: 2.9990 chunk 344 optimal weight: 5.9990 chunk 389 optimal weight: 0.8980 chunk 195 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 251 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 235 optimal weight: 10.0000 chunk 354 optimal weight: 2.9990 chunk 64 optimal weight: 0.0470 chunk 13 optimal weight: 9.9990 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 761 GLN A 972 HIS ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 761 GLN B 972 HIS C 761 GLN ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 972 HIS D 135 GLN D 761 GLN ** D 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 972 HIS ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.134378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.104215 restraints weight = 35748.773| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.55 r_work: 0.3150 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 32424 Z= 0.128 Angle : 0.538 7.090 44224 Z= 0.287 Chirality : 0.045 0.164 4644 Planarity : 0.004 0.047 5820 Dihedral : 5.252 53.656 4296 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.79 % Allowed : 13.91 % Favored : 84.30 % 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: 0.46 (0.13), residues: 3904 helix: 0.67 (0.22), residues: 532 sheet: 1.08 (0.14), residues: 1316 loop : -0.26 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 557 TYR 0.012 0.001 TYR B 906 PHE 0.011 0.001 PHE A 274 TRP 0.032 0.001 TRP D 553 HIS 0.008 0.001 HIS D 974 Details of bonding type rmsd covalent geometry : bond 0.00274 (32424) covalent geometry : angle 0.53850 (44224) hydrogen bonds : bond 0.04076 ( 1125) hydrogen bonds : angle 4.92698 ( 3144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7808 Ramachandran restraints generated. 3904 Oldfield, 0 Emsley, 3904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7808 Ramachandran restraints generated. 3904 Oldfield, 0 Emsley, 3904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 416 time to evaluate : 1.317 Fit side-chains REVERT: A 59 ARG cc_start: 0.8520 (mmm-85) cc_final: 0.8257 (mmm-85) REVERT: A 67 GLU cc_start: 0.8048 (mp0) cc_final: 0.7682 (mp0) REVERT: A 135 GLN cc_start: 0.7498 (mm-40) cc_final: 0.7190 (mt0) REVERT: A 423 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7755 (ttp) REVERT: A 859 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7438 (p0) REVERT: A 863 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7166 (mt0) REVERT: B 59 ARG cc_start: 0.8522 (mmm-85) cc_final: 0.8252 (mmm-85) REVERT: B 67 GLU cc_start: 0.8026 (mp0) cc_final: 0.7666 (mp0) REVERT: B 135 GLN cc_start: 0.7549 (mm-40) cc_final: 0.7134 (mt0) REVERT: B 423 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7752 (ttp) REVERT: B 859 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7426 (p0) REVERT: B 863 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7167 (mt0) REVERT: B 864 MET cc_start: 0.9035 (ttt) cc_final: 0.8687 (ttt) REVERT: C 59 ARG cc_start: 0.8394 (mmm-85) cc_final: 0.8146 (mmm-85) REVERT: C 67 GLU cc_start: 0.8042 (mp0) cc_final: 0.7682 (mp0) REVERT: C 135 GLN cc_start: 0.7538 (mm-40) cc_final: 0.7213 (mt0) REVERT: C 423 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7742 (ttp) REVERT: C 859 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7449 (p0) REVERT: C 863 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7180 (mt0) REVERT: C 864 MET cc_start: 0.9012 (ttt) cc_final: 0.8666 (ttt) REVERT: D 59 ARG cc_start: 0.8529 (mmm-85) cc_final: 0.8262 (mmm-85) REVERT: D 67 GLU cc_start: 0.8055 (mp0) cc_final: 0.7678 (mp0) REVERT: D 135 GLN cc_start: 0.7561 (mm-40) cc_final: 0.7091 (mt0) REVERT: D 205 MET cc_start: 0.7119 (OUTLIER) cc_final: 0.6916 (mmm) REVERT: D 423 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7750 (tpp) REVERT: D 859 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7440 (p0) REVERT: D 863 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7159 (mt0) outliers start: 60 outliers final: 34 residues processed: 446 average time/residue: 0.8656 time to fit residues: 448.0648 Evaluate side-chains 443 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 396 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 817 GLN Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 859 ASP Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 423 MET Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 768 MET Chi-restraints excluded: chain D residue 817 GLN Chi-restraints excluded: chain D residue 859 ASP Chi-restraints excluded: chain D residue 861 SER Chi-restraints excluded: chain D residue 863 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 277 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 209 optimal weight: 10.0000 chunk 342 optimal weight: 4.9990 chunk 184 optimal weight: 9.9990 chunk 230 optimal weight: 9.9990 chunk 365 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 23 optimal weight: 0.6980 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 HIS A 761 GLN A 972 HIS B 653 HIS B 761 GLN B 972 HIS C 653 HIS C 761 GLN C 972 HIS D 653 HIS D 761 GLN ** D 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 972 HIS ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.130646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.100289 restraints weight = 35898.788| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.54 r_work: 0.3090 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 32424 Z= 0.295 Angle : 0.705 8.775 44224 Z= 0.378 Chirality : 0.052 0.219 4644 Planarity : 0.006 0.082 5820 Dihedral : 5.981 58.752 4296 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.39 % Allowed : 13.46 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.28 (0.13), residues: 3904 helix: 0.21 (0.22), residues: 532 sheet: 1.05 (0.14), residues: 1304 loop : -0.35 (0.14), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 557 TYR 0.019 0.002 TYR D 906 PHE 0.019 0.003 PHE A 274 TRP 0.035 0.003 TRP C 553 HIS 0.010 0.002 HIS A 974 Details of bonding type rmsd covalent geometry : bond 0.00668 (32424) covalent geometry : angle 0.70489 (44224) hydrogen bonds : bond 0.05609 ( 1125) hydrogen bonds : angle 5.33835 ( 3144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7808 Ramachandran restraints generated. 3904 Oldfield, 0 Emsley, 3904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7808 Ramachandran restraints generated. 3904 Oldfield, 0 Emsley, 3904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 396 time to evaluate : 1.376 Fit side-chains REVERT: A 67 GLU cc_start: 0.8079 (mp0) cc_final: 0.7766 (mp0) REVERT: A 80 GLU cc_start: 0.4726 (OUTLIER) cc_final: 0.4462 (pm20) REVERT: A 135 GLN cc_start: 0.7524 (mm-40) cc_final: 0.7134 (mt0) REVERT: A 769 TRP cc_start: 0.7786 (OUTLIER) cc_final: 0.6627 (m100) REVERT: B 67 GLU cc_start: 0.8057 (mp0) cc_final: 0.7741 (mp0) REVERT: B 80 GLU cc_start: 0.4701 (OUTLIER) cc_final: 0.4422 (pm20) REVERT: B 135 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7142 (mt0) REVERT: B 769 TRP cc_start: 0.7772 (OUTLIER) cc_final: 0.6630 (m100) REVERT: C 59 ARG cc_start: 0.8405 (mmm-85) cc_final: 0.8149 (mmm-85) REVERT: C 67 GLU cc_start: 0.8056 (mp0) cc_final: 0.7749 (mp0) REVERT: C 769 TRP cc_start: 0.7785 (OUTLIER) cc_final: 0.6630 (m100) REVERT: D 67 GLU cc_start: 0.8087 (mp0) cc_final: 0.7782 (mp0) REVERT: D 80 GLU cc_start: 0.4688 (OUTLIER) cc_final: 0.4424 (pm20) REVERT: D 135 GLN cc_start: 0.7699 (mm-40) cc_final: 0.7123 (mt0) REVERT: D 769 TRP cc_start: 0.7785 (OUTLIER) cc_final: 0.6628 (m100) outliers start: 80 outliers final: 52 residues processed: 447 average time/residue: 0.8635 time to fit residues: 448.3015 Evaluate side-chains 439 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 380 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 769 TRP Chi-restraints excluded: chain A residue 817 GLN Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 769 TRP Chi-restraints excluded: chain B residue 817 GLN Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 859 ASP Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 769 TRP Chi-restraints excluded: chain C residue 817 GLN Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 904 GLU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 768 MET Chi-restraints excluded: chain D residue 769 TRP Chi-restraints excluded: chain D residue 817 GLN Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain D residue 859 ASP Chi-restraints excluded: chain D residue 861 SER Chi-restraints excluded: chain D residue 904 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 228 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 336 optimal weight: 0.6980 chunk 314 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 384 optimal weight: 4.9990 chunk 329 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 350 optimal weight: 6.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 HIS A 761 GLN A 972 HIS B 614 HIS B 761 GLN B 972 HIS C 135 GLN C 614 HIS C 761 GLN C 972 HIS D 761 GLN ** D 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 972 HIS ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.131796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.101528 restraints weight = 35775.744| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.54 r_work: 0.3110 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 32424 Z= 0.203 Angle : 0.627 8.100 44224 Z= 0.336 Chirality : 0.048 0.181 4644 Planarity : 0.005 0.065 5820 Dihedral : 5.810 57.334 4296 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.70 % Allowed : 14.44 % Favored : 83.85 % 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: 0.27 (0.13), residues: 3904 helix: 0.24 (0.22), residues: 532 sheet: 1.02 (0.14), residues: 1304 loop : -0.35 (0.14), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 557 TYR 0.015 0.002 TYR B 906 PHE 0.015 0.002 PHE A 274 TRP 0.037 0.002 TRP D 553 HIS 0.009 0.001 HIS A 974 Details of bonding type rmsd covalent geometry : bond 0.00452 (32424) covalent geometry : angle 0.62672 (44224) hydrogen bonds : bond 0.04966 ( 1125) hydrogen bonds : angle 5.23182 ( 3144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7808 Ramachandran restraints generated. 3904 Oldfield, 0 Emsley, 3904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7808 Ramachandran restraints generated. 3904 Oldfield, 0 Emsley, 3904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 402 time to evaluate : 1.320 Fit side-chains REVERT: A 67 GLU cc_start: 0.8084 (mp0) cc_final: 0.7689 (mp0) REVERT: A 80 GLU cc_start: 0.4650 (OUTLIER) cc_final: 0.4382 (pm20) REVERT: A 135 GLN cc_start: 0.7521 (mm-40) cc_final: 0.7189 (mt0) REVERT: A 859 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7399 (p0) REVERT: A 1022 GLN cc_start: 0.7752 (mp10) cc_final: 0.7547 (mp10) REVERT: B 67 GLU cc_start: 0.8065 (mp0) cc_final: 0.7674 (mp0) REVERT: B 135 GLN cc_start: 0.7566 (mm-40) cc_final: 0.7170 (mt0) REVERT: B 801 ILE cc_start: 0.6746 (OUTLIER) cc_final: 0.6354 (tt) REVERT: B 859 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7403 (p0) REVERT: C 59 ARG cc_start: 0.8371 (mmm-85) cc_final: 0.8127 (mmm-85) REVERT: C 67 GLU cc_start: 0.8034 (mp0) cc_final: 0.7624 (mp0) REVERT: C 80 GLU cc_start: 0.4694 (OUTLIER) cc_final: 0.4395 (pm20) REVERT: C 135 GLN cc_start: 0.7536 (mm-40) cc_final: 0.7134 (mt0) REVERT: C 859 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7407 (p0) REVERT: D 67 GLU cc_start: 0.8076 (mp0) cc_final: 0.7666 (mp0) REVERT: D 80 GLU cc_start: 0.4658 (OUTLIER) cc_final: 0.4387 (pm20) REVERT: D 135 GLN cc_start: 0.7654 (mm-40) cc_final: 0.7174 (mt0) REVERT: D 205 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.7051 (mmm) REVERT: D 859 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7407 (p0) REVERT: D 1022 GLN cc_start: 0.7755 (mp10) cc_final: 0.7548 (mp10) outliers start: 57 outliers final: 39 residues processed: 435 average time/residue: 0.8582 time to fit residues: 432.8981 Evaluate side-chains 434 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 386 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 817 GLN Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 817 GLN Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 859 ASP Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 817 GLN Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 768 MET Chi-restraints excluded: chain D residue 817 GLN Chi-restraints excluded: chain D residue 859 ASP Chi-restraints excluded: chain D residue 861 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 252 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 303 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 332 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 HIS A 653 HIS A 761 GLN A 972 HIS B 614 HIS B 653 HIS B 761 GLN B 972 HIS C 614 HIS C 761 GLN C 972 HIS D 653 HIS D 761 GLN D 885 ASN D 972 HIS D 985 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.131239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.100945 restraints weight = 35691.171| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.53 r_work: 0.3100 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 32424 Z= 0.237 Angle : 0.660 8.335 44224 Z= 0.354 Chirality : 0.050 0.196 4644 Planarity : 0.005 0.071 5820 Dihedral : 5.933 57.992 4296 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.76 % Allowed : 14.53 % Favored : 83.70 % 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: 0.23 (0.13), residues: 3904 helix: 0.16 (0.22), residues: 532 sheet: 1.01 (0.14), residues: 1304 loop : -0.37 (0.14), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 557 TYR 0.016 0.002 TYR B 906 PHE 0.016 0.002 PHE A 274 TRP 0.037 0.002 TRP A 553 HIS 0.009 0.002 HIS D 974 Details of bonding type rmsd covalent geometry : bond 0.00531 (32424) covalent geometry : angle 0.66004 (44224) hydrogen bonds : bond 0.05236 ( 1125) hydrogen bonds : angle 5.29070 ( 3144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7808 Ramachandran restraints generated. 3904 Oldfield, 0 Emsley, 3904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7808 Ramachandran restraints generated. 3904 Oldfield, 0 Emsley, 3904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 392 time to evaluate : 1.234 Fit side-chains REVERT: A 67 GLU cc_start: 0.8078 (mp0) cc_final: 0.7784 (mp0) REVERT: A 135 GLN cc_start: 0.7535 (mm-40) cc_final: 0.7147 (mt0) REVERT: A 423 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7990 (ttp) REVERT: A 859 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7355 (p0) REVERT: A 864 MET cc_start: 0.9020 (ttt) cc_final: 0.8571 (ttt) REVERT: B 67 GLU cc_start: 0.8062 (mp0) cc_final: 0.7764 (mp0) REVERT: B 135 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7157 (mt0) REVERT: B 423 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7949 (ttp) REVERT: B 801 ILE cc_start: 0.6746 (OUTLIER) cc_final: 0.6356 (tt) REVERT: B 859 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7372 (p0) REVERT: B 864 MET cc_start: 0.9023 (ttt) cc_final: 0.8577 (ttt) REVERT: C 59 ARG cc_start: 0.8385 (mmm-85) cc_final: 0.8147 (mmm-85) REVERT: C 67 GLU cc_start: 0.8054 (mp0) cc_final: 0.7755 (mp0) REVERT: C 135 GLN cc_start: 0.7554 (mm-40) cc_final: 0.7136 (mt0) REVERT: C 423 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7936 (ttp) REVERT: C 859 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7371 (p0) REVERT: C 864 MET cc_start: 0.9013 (ttt) cc_final: 0.8557 (ttt) REVERT: D 67 GLU cc_start: 0.8087 (mp0) cc_final: 0.7797 (mp0) REVERT: D 135 GLN cc_start: 0.7640 (mm-40) cc_final: 0.7143 (mt0) REVERT: D 205 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.7136 (mmm) REVERT: D 859 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7356 (p0) REVERT: D 864 MET cc_start: 0.9017 (ttt) cc_final: 0.8564 (ttt) outliers start: 59 outliers final: 41 residues processed: 424 average time/residue: 0.8599 time to fit residues: 422.4771 Evaluate side-chains 430 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 380 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 817 GLN Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 817 GLN Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 859 ASP Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 817 GLN Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 904 GLU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 768 MET Chi-restraints excluded: chain D residue 817 GLN Chi-restraints excluded: chain D residue 859 ASP Chi-restraints excluded: chain D residue 861 SER Chi-restraints excluded: chain D residue 904 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 55 optimal weight: 1.9990 chunk 213 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 226 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 297 optimal weight: 2.9990 chunk 370 optimal weight: 3.9990 chunk 209 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 225 optimal weight: 0.5980 chunk 289 optimal weight: 7.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 761 GLN ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 972 HIS ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 761 GLN B 972 HIS C 761 GLN C 972 HIS D 761 GLN ** D 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 972 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.132726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.102443 restraints weight = 36014.291| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.55 r_work: 0.3125 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 32424 Z= 0.161 Angle : 0.584 7.587 44224 Z= 0.313 Chirality : 0.046 0.174 4644 Planarity : 0.005 0.054 5820 Dihedral : 5.639 55.996 4296 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.76 % Allowed : 14.29 % Favored : 83.94 % 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: 0.34 (0.13), residues: 3904 helix: 0.36 (0.22), residues: 532 sheet: 1.04 (0.14), residues: 1316 loop : -0.31 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 557 TYR 0.013 0.002 TYR D 906 PHE 0.012 0.002 PHE A 274 TRP 0.039 0.002 TRP B 553 HIS 0.008 0.001 HIS D 974 Details of bonding type rmsd covalent geometry : bond 0.00355 (32424) covalent geometry : angle 0.58408 (44224) hydrogen bonds : bond 0.04504 ( 1125) hydrogen bonds : angle 5.11842 ( 3144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7808 Ramachandran restraints generated. 3904 Oldfield, 0 Emsley, 3904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7808 Ramachandran restraints generated. 3904 Oldfield, 0 Emsley, 3904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 398 time to evaluate : 1.326 Fit side-chains REVERT: A 67 GLU cc_start: 0.8084 (mp0) cc_final: 0.7708 (mp0) REVERT: A 135 GLN cc_start: 0.7572 (mm-40) cc_final: 0.7205 (mt0) REVERT: A 859 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7382 (p0) REVERT: A 863 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7139 (mt0) REVERT: A 864 MET cc_start: 0.8974 (ttt) cc_final: 0.8496 (ttt) REVERT: B 59 ARG cc_start: 0.8573 (mmm-85) cc_final: 0.8307 (mmm-85) REVERT: B 67 GLU cc_start: 0.8058 (mp0) cc_final: 0.7684 (mp0) REVERT: B 135 GLN cc_start: 0.7566 (mm-40) cc_final: 0.7166 (mt0) REVERT: B 423 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7813 (ttp) REVERT: B 801 ILE cc_start: 0.6695 (OUTLIER) cc_final: 0.6344 (tt) REVERT: B 859 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7379 (p0) REVERT: B 863 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7197 (mt0) REVERT: B 864 MET cc_start: 0.8971 (ttt) cc_final: 0.8493 (ttt) REVERT: C 59 ARG cc_start: 0.8382 (mmm-85) cc_final: 0.8155 (mmm-85) REVERT: C 67 GLU cc_start: 0.8059 (mp0) cc_final: 0.7670 (mp0) REVERT: C 135 GLN cc_start: 0.7567 (mm-40) cc_final: 0.7180 (mt0) REVERT: C 423 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7805 (ttp) REVERT: C 859 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7381 (p0) REVERT: C 863 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7170 (mt0) REVERT: C 864 MET cc_start: 0.8963 (ttt) cc_final: 0.8479 (ttt) REVERT: D 67 GLU cc_start: 0.8090 (mp0) cc_final: 0.7696 (mp0) REVERT: D 135 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7149 (mt0) REVERT: D 859 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7379 (p0) REVERT: D 863 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.7139 (mt0) REVERT: D 864 MET cc_start: 0.8969 (ttt) cc_final: 0.8486 (ttt) outliers start: 59 outliers final: 39 residues processed: 431 average time/residue: 0.8708 time to fit residues: 435.5764 Evaluate side-chains 433 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 383 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 817 GLN Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 817 GLN Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 859 ASP Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 817 GLN Chi-restraints excluded: chain C residue 859 ASP Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain C residue 904 GLU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 768 MET Chi-restraints excluded: chain D residue 859 ASP Chi-restraints excluded: chain D residue 861 SER Chi-restraints excluded: chain D residue 863 GLN Chi-restraints excluded: chain D residue 904 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 213 optimal weight: 2.9990 chunk 364 optimal weight: 0.8980 chunk 227 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 229 optimal weight: 4.9990 chunk 304 optimal weight: 0.0570 chunk 144 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 160 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 overall best weight: 1.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN A 761 GLN ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 972 HIS ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 761 GLN B 972 HIS C 761 GLN ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 972 HIS D 365 GLN D 761 GLN ** D 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 972 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.134301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.104242 restraints weight = 35776.616| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.55 r_work: 0.3152 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 32424 Z= 0.124 Angle : 0.544 7.016 44224 Z= 0.291 Chirality : 0.045 0.166 4644 Planarity : 0.004 0.050 5820 Dihedral : 5.353 53.853 4296 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.56 % Allowed : 14.62 % Favored : 83.82 % 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: 0.41 (0.13), residues: 3904 helix: 0.57 (0.22), residues: 532 sheet: 1.03 (0.14), residues: 1316 loop : -0.27 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 59 TYR 0.011 0.001 TYR B 906 PHE 0.011 0.001 PHE A 274 TRP 0.039 0.002 TRP B 553 HIS 0.007 0.001 HIS C 974 Details of bonding type rmsd covalent geometry : bond 0.00267 (32424) covalent geometry : angle 0.54410 (44224) hydrogen bonds : bond 0.04013 ( 1125) hydrogen bonds : angle 4.94939 ( 3144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16749.57 seconds wall clock time: 285 minutes 16.21 seconds (17116.21 seconds total)