Starting phenix.real_space_refine on Wed Mar 20 15:33:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lve_0991/03_2024/6lve_0991.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lve_0991/03_2024/6lve_0991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lve_0991/03_2024/6lve_0991.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lve_0991/03_2024/6lve_0991.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lve_0991/03_2024/6lve_0991.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lve_0991/03_2024/6lve_0991.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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 96 5.16 5 C 17476 2.51 5 N 4856 2.21 5 O 5268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 299": "NH1" <-> "NH2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 108": "NH1" <-> "NH2" Residue "C TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 299": "NH1" <-> "NH2" Residue "C TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 108": "NH1" <-> "NH2" Residue "E TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E ARG 120": "NH1" <-> "NH2" Residue "E PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 299": "NH1" <-> "NH2" Residue "E TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G ARG 120": "NH1" <-> "NH2" Residue "G TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 299": "NH1" <-> "NH2" Residue "G PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 108": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27696 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5907 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 39, 'TRANS': 711} Chain breaks: 2 Chain: "B" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1017 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 5907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5907 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 39, 'TRANS': 711} Chain breaks: 2 Chain: "D" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1017 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 5907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5907 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 39, 'TRANS': 711} Chain breaks: 2 Chain: "F" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1017 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 5907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5907 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 39, 'TRANS': 711} Chain breaks: 2 Chain: "H" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1017 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 13.69, per 1000 atoms: 0.49 Number of scatterers: 27696 At special positions: 0 Unit cell: (120.91, 155.15, 105.93, 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 96 16.00 O 5268 8.00 N 4856 7.00 C 17476 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 - 3.50 Amino acid : False - 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: 9.72 Conformation dependent library (CDL) restraints added in 5.8 seconds 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6320 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 34 sheets defined 23.9% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.34 Creating SS restraints... Processing helix chain 'A' and resid 224 through 228 removed outlier: 3.899A pdb=" N GLY A 227 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 259 removed outlier: 3.514A pdb=" N ARG A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 removed outlier: 3.543A pdb=" N GLN A 326 " --> pdb=" O CYS A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 399 removed outlier: 3.525A pdb=" N TYR A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.871A pdb=" N ILE A 410 " --> pdb=" O LYS A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 431 removed outlier: 3.706A pdb=" N GLU A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 462 removed outlier: 4.038A pdb=" N ARG A 462 " --> pdb=" O MET A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 removed outlier: 4.276A pdb=" N LEU A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 504 Processing helix chain 'A' and resid 504 through 509 removed outlier: 4.159A pdb=" N LEU A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 537 removed outlier: 3.818A pdb=" N ASP A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 597 Processing helix chain 'A' and resid 599 through 605 removed outlier: 3.965A pdb=" N ILE A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 631 removed outlier: 3.775A pdb=" N GLN A 626 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLU A 628 " --> pdb=" O SER A 625 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ARG A 629 " --> pdb=" O GLN A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 733 removed outlier: 3.832A pdb=" N TRP A 729 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 730 " --> pdb=" O ILE A 727 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 733 " --> pdb=" O LEU A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 754 Processing helix chain 'B' and resid 19 through 41 Processing helix chain 'B' and resid 43 through 51 Processing helix chain 'B' and resid 60 through 71 Processing helix chain 'B' and resid 73 through 78 removed outlier: 3.697A pdb=" N GLY B 77 " --> pdb=" O PRO B 74 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG B 78 " --> pdb=" O THR B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 130 Processing helix chain 'C' and resid 224 through 228 removed outlier: 3.577A pdb=" N GLY C 227 " --> pdb=" O ALA C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 323 through 327 Processing helix chain 'C' and resid 393 through 399 removed outlier: 3.890A pdb=" N TYR C 399 " --> pdb=" O SER C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.517A pdb=" N ALA C 408 " --> pdb=" O MET C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 431 removed outlier: 3.683A pdb=" N LEU C 428 " --> pdb=" O ASN C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 435 Processing helix chain 'C' and resid 458 through 462 removed outlier: 4.120A pdb=" N ARG C 462 " --> pdb=" O MET C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 488 removed outlier: 4.352A pdb=" N LEU C 481 " --> pdb=" O ALA C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 504 Processing helix chain 'C' and resid 504 through 509 removed outlier: 4.086A pdb=" N LEU C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 537 removed outlier: 3.961A pdb=" N ASP C 537 " --> pdb=" O ASP C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 597 Processing helix chain 'C' and resid 599 through 603 Processing helix chain 'C' and resid 623 through 627 Processing helix chain 'C' and resid 662 through 666 removed outlier: 3.527A pdb=" N LEU C 665 " --> pdb=" O ASP C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 718 No H-bonds generated for 'chain 'C' and resid 716 through 718' Processing helix chain 'C' and resid 726 through 730 removed outlier: 3.629A pdb=" N TRP C 729 " --> pdb=" O SER C 726 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 730 " --> pdb=" O ILE C 727 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 726 through 730' Processing helix chain 'C' and resid 740 through 754 Processing helix chain 'D' and resid 18 through 41 removed outlier: 4.225A pdb=" N TRP D 22 " --> pdb=" O ARG D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 51 Processing helix chain 'D' and resid 60 through 71 Processing helix chain 'D' and resid 72 through 78 removed outlier: 6.227A pdb=" N THR D 75 " --> pdb=" O MET D 72 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY D 77 " --> pdb=" O PRO D 74 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG D 78 " --> pdb=" O THR D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 130 removed outlier: 3.686A pdb=" N ALA D 115 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU D 130 " --> pdb=" O ASP D 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 228 removed outlier: 3.578A pdb=" N GLY E 227 " --> pdb=" O ALA E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 258 Processing helix chain 'E' and resid 264 through 266 No H-bonds generated for 'chain 'E' and resid 264 through 266' Processing helix chain 'E' and resid 323 through 327 Processing helix chain 'E' and resid 393 through 399 removed outlier: 3.890A pdb=" N TYR E 399 " --> pdb=" O SER E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 408 removed outlier: 3.558A pdb=" N ALA E 408 " --> pdb=" O MET E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 431 removed outlier: 3.682A pdb=" N LEU E 428 " --> pdb=" O ASN E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 435 Processing helix chain 'E' and resid 458 through 462 removed outlier: 4.119A pdb=" N ARG E 462 " --> pdb=" O MET E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 488 removed outlier: 4.351A pdb=" N LEU E 481 " --> pdb=" O ALA E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 504 Processing helix chain 'E' and resid 504 through 509 removed outlier: 4.087A pdb=" N LEU E 508 " --> pdb=" O GLY E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 537 removed outlier: 4.007A pdb=" N ASP E 537 " --> pdb=" O ASP E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 593 through 597 Processing helix chain 'E' and resid 599 through 603 Processing helix chain 'E' and resid 623 through 627 Processing helix chain 'E' and resid 662 through 666 removed outlier: 3.527A pdb=" N LEU E 665 " --> pdb=" O ASP E 662 " (cutoff:3.500A) Processing helix chain 'E' and resid 688 through 691 removed outlier: 3.749A pdb=" N LYS E 691 " --> pdb=" O PRO E 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 688 through 691' Processing helix chain 'E' and resid 716 through 718 No H-bonds generated for 'chain 'E' and resid 716 through 718' Processing helix chain 'E' and resid 726 through 730 removed outlier: 3.626A pdb=" N TRP E 729 " --> pdb=" O SER E 726 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU E 730 " --> pdb=" O ILE E 727 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 726 through 730' Processing helix chain 'E' and resid 740 through 754 Processing helix chain 'F' and resid 18 through 41 removed outlier: 4.225A pdb=" N TRP F 22 " --> pdb=" O ARG F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 51 Processing helix chain 'F' and resid 60 through 71 Processing helix chain 'F' and resid 72 through 78 removed outlier: 6.227A pdb=" N THR F 75 " --> pdb=" O MET F 72 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY F 77 " --> pdb=" O PRO F 74 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG F 78 " --> pdb=" O THR F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 130 removed outlier: 3.654A pdb=" N ALA F 115 " --> pdb=" O THR F 111 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU F 130 " --> pdb=" O ASP F 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 228 removed outlier: 3.960A pdb=" N GLY G 227 " --> pdb=" O ALA G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 259 removed outlier: 3.515A pdb=" N ARG G 259 " --> pdb=" O GLU G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 327 removed outlier: 3.543A pdb=" N GLN G 326 " --> pdb=" O CYS G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 392 through 399 removed outlier: 3.525A pdb=" N TYR G 399 " --> pdb=" O SER G 395 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 410 removed outlier: 3.919A pdb=" N ILE G 410 " --> pdb=" O LYS G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 422 through 431 removed outlier: 3.706A pdb=" N GLU G 427 " --> pdb=" O GLU G 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 458 through 462 removed outlier: 4.032A pdb=" N ARG G 462 " --> pdb=" O MET G 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 488 removed outlier: 4.275A pdb=" N LEU G 481 " --> pdb=" O ALA G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 504 Processing helix chain 'G' and resid 504 through 509 removed outlier: 4.162A pdb=" N LEU G 508 " --> pdb=" O GLY G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 525 through 537 removed outlier: 3.818A pdb=" N ASP G 537 " --> pdb=" O ASP G 533 " (cutoff:3.500A) Processing helix chain 'G' and resid 593 through 597 Processing helix chain 'G' and resid 599 through 605 removed outlier: 3.966A pdb=" N ILE G 603 " --> pdb=" O ALA G 599 " (cutoff:3.500A) Processing helix chain 'G' and resid 623 through 631 removed outlier: 3.774A pdb=" N GLN G 626 " --> pdb=" O PRO G 623 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLU G 628 " --> pdb=" O SER G 625 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ARG G 629 " --> pdb=" O GLN G 626 " (cutoff:3.500A) Processing helix chain 'G' and resid 726 through 733 removed outlier: 3.832A pdb=" N TRP G 729 " --> pdb=" O SER G 726 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU G 730 " --> pdb=" O ILE G 727 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU G 733 " --> pdb=" O LEU G 730 " (cutoff:3.500A) Processing helix chain 'G' and resid 740 through 754 Processing helix chain 'H' and resid 19 through 41 Processing helix chain 'H' and resid 43 through 51 Processing helix chain 'H' and resid 60 through 71 Processing helix chain 'H' and resid 73 through 78 removed outlier: 3.692A pdb=" N GLY H 77 " --> pdb=" O PRO H 74 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG H 78 " --> pdb=" O THR H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 130 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 15 removed outlier: 4.941A pdb=" N PHE A 358 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU A 41 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU A 56 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 14 through 15 removed outlier: 4.941A pdb=" N PHE A 358 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY A 64 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 148 removed outlier: 6.924A pdb=" N SER A 122 " --> pdb=" O TRP A 116 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N TRP A 116 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TRP A 124 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER A 114 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU A 126 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 288 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL A 289 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE A 244 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N HIS A 271 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ASP A 273 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 10.017A pdb=" N ASP A 240 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL A 239 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N TRP A 101 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ALA A 241 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE A 99 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 95 " --> pdb=" O TYR A 245 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 144 through 148 removed outlier: 6.924A pdb=" N SER A 122 " --> pdb=" O TRP A 116 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N TRP A 116 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TRP A 124 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER A 114 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU A 126 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 288 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL A 289 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE A 244 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N HIS A 271 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ASP A 273 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 10.017A pdb=" N ASP A 240 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 330 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.748A pdb=" N ILE A 387 " --> pdb=" O ASP A 493 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ALA A 495 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL A 389 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU A 388 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 514 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE A 710 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 618 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 12.388A pdb=" N PHE A 611 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 12.534A pdb=" N ARG A 660 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 11.967A pdb=" N PHE A 613 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 12.506A pdb=" N LEU A 658 " --> pdb=" O PHE A 613 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N HIS A 615 " --> pdb=" O TYR A 656 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR A 656 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY A 654 " --> pdb=" O GLY A 617 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.748A pdb=" N ILE A 387 " --> pdb=" O ASP A 493 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ALA A 495 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL A 389 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU A 388 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 514 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE A 710 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 618 " --> pdb=" O VAL A 678 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 420 through 421 Processing sheet with id=AA9, first strand: chain 'A' and resid 451 through 453 Processing sheet with id=AB1, first strand: chain 'C' and resid 6 through 10 removed outlier: 3.694A pdb=" N PHE C 346 " --> pdb=" O PHE C 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 14 through 15 removed outlier: 4.940A pdb=" N PHE C 358 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU C 38 " --> pdb=" O ILE C 58 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LYS C 54 " --> pdb=" O ILE C 42 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 14 through 15 removed outlier: 4.940A pdb=" N PHE C 358 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA C 36 " --> pdb=" O GLY C 64 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY C 64 " --> pdb=" O ALA C 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 144 through 148 removed outlier: 3.522A pdb=" N SER C 122 " --> pdb=" O ASN C 117 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE C 128 " --> pdb=" O GLY C 111 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLY C 111 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 288 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL C 289 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE C 244 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N HIS C 271 " --> pdb=" O PRO C 242 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ASP C 273 " --> pdb=" O ASP C 240 " (cutoff:3.500A) removed outlier: 10.063A pdb=" N ASP C 240 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N VAL C 239 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TRP C 101 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ALA C 241 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N PHE C 99 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.613A pdb=" N LEU C 388 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL C 514 " --> pdb=" O MET C 542 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE C 710 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR C 618 " --> pdb=" O VAL C 678 " (cutoff:3.500A) removed outlier: 12.449A pdb=" N PHE C 611 " --> pdb=" O ARG C 660 " (cutoff:3.500A) removed outlier: 12.255A pdb=" N ARG C 660 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 11.857A pdb=" N PHE C 613 " --> pdb=" O LEU C 658 " (cutoff:3.500A) removed outlier: 12.650A pdb=" N LEU C 658 " --> pdb=" O PHE C 613 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N HIS C 615 " --> pdb=" O TYR C 656 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR C 656 " --> pdb=" O HIS C 615 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.613A pdb=" N LEU C 388 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL C 514 " --> pdb=" O MET C 542 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE C 710 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR C 618 " --> pdb=" O VAL C 678 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE C 611 " --> pdb=" O THR C 685 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 420 through 421 Processing sheet with id=AB8, first strand: chain 'C' and resid 451 through 453 removed outlier: 6.166A pdb=" N GLN C 523 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL C 555 " --> pdb=" O GLN C 523 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 6 through 10 removed outlier: 3.686A pdb=" N PHE E 346 " --> pdb=" O PHE E 23 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 14 through 15 removed outlier: 4.946A pdb=" N PHE E 358 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU E 38 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS E 54 " --> pdb=" O ILE E 42 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 14 through 15 removed outlier: 4.946A pdb=" N PHE E 358 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA E 36 " --> pdb=" O GLY E 64 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY E 64 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 144 through 148 removed outlier: 3.521A pdb=" N SER E 122 " --> pdb=" O ASN E 117 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE E 128 " --> pdb=" O GLY E 111 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLY E 111 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL E 288 " --> pdb=" O GLY E 298 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL E 289 " --> pdb=" O ASP E 273 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE E 244 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N HIS E 271 " --> pdb=" O PRO E 242 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N ASP E 273 " --> pdb=" O ASP E 240 " (cutoff:3.500A) removed outlier: 10.064A pdb=" N ASP E 240 " --> pdb=" O ASP E 273 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL E 239 " --> pdb=" O TRP E 101 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N TRP E 101 " --> pdb=" O VAL E 239 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ALA E 241 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N PHE E 99 " --> pdb=" O ALA E 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 492 through 496 removed outlier: 6.612A pdb=" N LEU E 388 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL E 514 " --> pdb=" O MET E 542 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE E 710 " --> pdb=" O LEU E 674 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR E 618 " --> pdb=" O VAL E 678 " (cutoff:3.500A) removed outlier: 12.448A pdb=" N PHE E 611 " --> pdb=" O ARG E 660 " (cutoff:3.500A) removed outlier: 12.257A pdb=" N ARG E 660 " --> pdb=" O PHE E 611 " (cutoff:3.500A) removed outlier: 11.855A pdb=" N PHE E 613 " --> pdb=" O LEU E 658 " (cutoff:3.500A) removed outlier: 12.649A pdb=" N LEU E 658 " --> pdb=" O PHE E 613 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N HIS E 615 " --> pdb=" O TYR E 656 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR E 656 " --> pdb=" O HIS E 615 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 642 through 643 removed outlier: 3.575A pdb=" N PHE E 611 " --> pdb=" O THR E 685 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 420 through 421 Processing sheet with id=AC7, first strand: chain 'E' and resid 451 through 453 removed outlier: 6.166A pdb=" N GLN E 523 " --> pdb=" O VAL E 553 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N VAL E 555 " --> pdb=" O GLN E 523 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 6 through 10 Processing sheet with id=AC9, first strand: chain 'G' and resid 14 through 15 removed outlier: 4.941A pdb=" N PHE G 358 " --> pdb=" O LEU G 41 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU G 41 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLU G 56 " --> pdb=" O LEU G 41 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 14 through 15 removed outlier: 4.941A pdb=" N PHE G 358 " --> pdb=" O LEU G 41 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY G 64 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 144 through 148 removed outlier: 6.923A pdb=" N SER G 122 " --> pdb=" O TRP G 116 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TRP G 116 " --> pdb=" O SER G 122 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TRP G 124 " --> pdb=" O SER G 114 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER G 114 " --> pdb=" O TRP G 124 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU G 126 " --> pdb=" O ILE G 112 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL G 288 " --> pdb=" O GLY G 298 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL G 289 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE G 244 " --> pdb=" O LEU G 269 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N HIS G 271 " --> pdb=" O PRO G 242 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N ASP G 273 " --> pdb=" O ASP G 240 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N ASP G 240 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL G 239 " --> pdb=" O TRP G 101 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N TRP G 101 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ALA G 241 " --> pdb=" O PHE G 99 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE G 99 " --> pdb=" O ALA G 241 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER G 95 " --> pdb=" O TYR G 245 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 144 through 148 removed outlier: 6.923A pdb=" N SER G 122 " --> pdb=" O TRP G 116 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TRP G 116 " --> pdb=" O SER G 122 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TRP G 124 " --> pdb=" O SER G 114 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER G 114 " --> pdb=" O TRP G 124 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU G 126 " --> pdb=" O ILE G 112 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL G 288 " --> pdb=" O GLY G 298 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL G 289 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE G 244 " --> pdb=" O LEU G 269 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N HIS G 271 " --> pdb=" O PRO G 242 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N ASP G 273 " --> pdb=" O ASP G 240 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N ASP G 240 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU G 330 " --> pdb=" O VAL G 239 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 492 through 496 removed outlier: 6.748A pdb=" N ILE G 387 " --> pdb=" O ASP G 493 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ALA G 495 " --> pdb=" O ILE G 387 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL G 389 " --> pdb=" O ALA G 495 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU G 388 " --> pdb=" O LEU G 515 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL G 514 " --> pdb=" O MET G 542 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE G 710 " --> pdb=" O LEU G 674 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR G 618 " --> pdb=" O VAL G 678 " (cutoff:3.500A) removed outlier: 12.376A pdb=" N PHE G 611 " --> pdb=" O ARG G 660 " (cutoff:3.500A) removed outlier: 12.540A pdb=" N ARG G 660 " --> pdb=" O PHE G 611 " (cutoff:3.500A) removed outlier: 11.933A pdb=" N PHE G 613 " --> pdb=" O LEU G 658 " (cutoff:3.500A) removed outlier: 12.477A pdb=" N LEU G 658 " --> pdb=" O PHE G 613 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N HIS G 615 " --> pdb=" O TYR G 656 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR G 656 " --> pdb=" O HIS G 615 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY G 654 " --> pdb=" O GLY G 617 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 492 through 496 removed outlier: 6.748A pdb=" N ILE G 387 " --> pdb=" O ASP G 493 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ALA G 495 " --> pdb=" O ILE G 387 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL G 389 " --> pdb=" O ALA G 495 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU G 388 " --> pdb=" O LEU G 515 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL G 514 " --> pdb=" O MET G 542 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE G 710 " --> pdb=" O LEU G 674 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR G 618 " --> pdb=" O VAL G 678 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 420 through 421 Processing sheet with id=AD7, first strand: chain 'G' and resid 451 through 453 1035 hydrogen bonds defined for protein. 2730 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: 11.93 Time building geometry restraints manager: 10.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7094 1.33 - 1.45: 6337 1.45 - 1.57: 14889 1.57 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 28476 Sorted by residual: bond pdb=" CA PRO A 668 " pdb=" C PRO A 668 " ideal model delta sigma weight residual 1.514 1.501 0.013 5.50e-03 3.31e+04 5.81e+00 bond pdb=" CG LEU C 330 " pdb=" CD1 LEU C 330 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.24e+00 bond pdb=" CG LEU E 330 " pdb=" CD1 LEU E 330 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.24e+00 bond pdb=" CG1 ILE A 161 " pdb=" CD1 ILE A 161 " ideal model delta sigma weight residual 1.513 1.430 0.083 3.90e-02 6.57e+02 4.56e+00 bond pdb=" CG1 ILE C 552 " pdb=" CD1 ILE C 552 " ideal model delta sigma weight residual 1.513 1.431 0.082 3.90e-02 6.57e+02 4.46e+00 ... (remaining 28471 not shown) Histogram of bond angle deviations from ideal: 97.19 - 104.57: 532 104.57 - 111.96: 12566 111.96 - 119.34: 10337 119.34 - 126.73: 14647 126.73 - 134.12: 610 Bond angle restraints: 38692 Sorted by residual: angle pdb=" N PHE E 332 " pdb=" CA PHE E 332 " pdb=" C PHE E 332 " ideal model delta sigma weight residual 110.91 117.62 -6.71 1.17e+00 7.31e-01 3.29e+01 angle pdb=" N PHE C 332 " pdb=" CA PHE C 332 " pdb=" C PHE C 332 " ideal model delta sigma weight residual 110.91 117.58 -6.67 1.17e+00 7.31e-01 3.25e+01 angle pdb=" C TYR C 656 " pdb=" N GLU C 657 " pdb=" CA GLU C 657 " ideal model delta sigma weight residual 121.54 131.32 -9.78 1.91e+00 2.74e-01 2.62e+01 angle pdb=" C TYR E 656 " pdb=" N GLU E 657 " pdb=" CA GLU E 657 " ideal model delta sigma weight residual 121.54 131.28 -9.74 1.91e+00 2.74e-01 2.60e+01 angle pdb=" C TYR G 656 " pdb=" N GLU G 657 " pdb=" CA GLU G 657 " ideal model delta sigma weight residual 121.54 130.80 -9.26 1.91e+00 2.74e-01 2.35e+01 ... (remaining 38687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.36: 15636 15.36 - 30.72: 804 30.72 - 46.08: 119 46.08 - 61.44: 17 61.44 - 76.80: 8 Dihedral angle restraints: 16584 sinusoidal: 6624 harmonic: 9960 Sorted by residual: dihedral pdb=" CA GLU E 19 " pdb=" C GLU E 19 " pdb=" N THR E 20 " pdb=" CA THR E 20 " ideal model delta harmonic sigma weight residual 180.00 -151.28 -28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA GLU C 19 " pdb=" C GLU C 19 " pdb=" N THR C 20 " pdb=" CA THR C 20 " ideal model delta harmonic sigma weight residual 180.00 -151.33 -28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA PRO C 577 " pdb=" C PRO C 577 " pdb=" N PRO C 578 " pdb=" CA PRO C 578 " ideal model delta harmonic sigma weight residual 180.00 -153.15 -26.85 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 16581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 3472 0.097 - 0.193: 440 0.193 - 0.290: 18 0.290 - 0.386: 6 0.386 - 0.483: 4 Chirality restraints: 3940 Sorted by residual: chirality pdb=" CB ILE A 283 " pdb=" CA ILE A 283 " pdb=" CG1 ILE A 283 " pdb=" CG2 ILE A 283 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.82e+00 chirality pdb=" CB ILE G 283 " pdb=" CA ILE G 283 " pdb=" CG1 ILE G 283 " pdb=" CG2 ILE G 283 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.76e+00 chirality pdb=" CB ILE E 283 " pdb=" CA ILE E 283 " pdb=" CG1 ILE E 283 " pdb=" CG2 ILE E 283 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.47e+00 ... (remaining 3937 not shown) Planarity restraints: 5132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 331 " -0.026 2.00e-02 2.50e+03 2.19e-02 1.20e+01 pdb=" CG TRP A 331 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP A 331 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 331 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 331 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 331 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 331 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 331 " -0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 331 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 331 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 331 " -0.025 2.00e-02 2.50e+03 2.10e-02 1.10e+01 pdb=" CG TRP G 331 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP G 331 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP G 331 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP G 331 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP G 331 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 331 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 331 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 331 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP G 331 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 331 " 0.028 2.00e-02 2.50e+03 2.06e-02 1.06e+01 pdb=" CG TRP E 331 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP E 331 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP E 331 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP E 331 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP E 331 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 331 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 331 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 331 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP E 331 " 0.002 2.00e-02 2.50e+03 ... (remaining 5129 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5805 2.77 - 3.30: 23548 3.30 - 3.84: 47114 3.84 - 4.37: 58855 4.37 - 4.90: 101465 Nonbonded interactions: 236787 Sorted by model distance: nonbonded pdb=" O HIS E 615 " pdb=" OH TYR E 684 " model vdw 2.239 2.440 nonbonded pdb=" O HIS C 615 " pdb=" OH TYR C 684 " model vdw 2.242 2.440 nonbonded pdb=" OH TYR E 396 " pdb=" OD2 ASP E 478 " model vdw 2.243 2.440 nonbonded pdb=" OH TYR C 396 " pdb=" OD2 ASP C 478 " model vdw 2.244 2.440 nonbonded pdb=" OH TYR G 396 " pdb=" OD2 ASP G 478 " model vdw 2.282 2.440 ... (remaining 236782 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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: 1.540 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: 8.600 Check model and map are aligned: 0.410 Set scattering table: 0.230 Process input model: 72.820 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.170 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 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 : 0.011 0.083 28476 Z= 0.716 Angle : 0.999 9.784 38692 Z= 0.555 Chirality : 0.065 0.483 3940 Planarity : 0.008 0.068 5132 Dihedral : 9.727 76.803 10264 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.42 % Allowed : 1.46 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.12), residues: 3440 helix: -2.61 (0.15), residues: 652 sheet: -1.07 (0.21), residues: 628 loop : -2.46 (0.11), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.004 TRP A 331 HIS 0.019 0.004 HIS G 556 PHE 0.037 0.005 PHE C 332 TYR 0.054 0.004 TYR G 684 ARG 0.013 0.002 ARG E 592 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 493 time to evaluate : 3.151 Fit side-chains REVERT: A 486 ASN cc_start: 0.8739 (m-40) cc_final: 0.8447 (m-40) REVERT: A 499 ASP cc_start: 0.7817 (m-30) cc_final: 0.7545 (m-30) REVERT: A 638 ASP cc_start: 0.7017 (t70) cc_final: 0.6401 (t70) REVERT: B 17 ASP cc_start: 0.8585 (t0) cc_final: 0.8381 (t70) REVERT: B 111 THR cc_start: 0.8175 (p) cc_final: 0.7915 (t) REVERT: B 116 MET cc_start: 0.8104 (mtt) cc_final: 0.7842 (mtm) REVERT: C 12 ARG cc_start: 0.8066 (ptm160) cc_final: 0.7843 (ptp-170) REVERT: C 58 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8603 (mp) REVERT: C 69 ARG cc_start: 0.7858 (ptt180) cc_final: 0.7607 (ptt180) REVERT: C 200 SER cc_start: 0.8854 (p) cc_final: 0.8570 (m) REVERT: C 638 ASP cc_start: 0.7045 (t70) cc_final: 0.6586 (m-30) REVERT: D 32 LYS cc_start: 0.8369 (mtmt) cc_final: 0.7930 (mttm) REVERT: D 36 ASP cc_start: 0.7185 (m-30) cc_final: 0.6745 (m-30) REVERT: E 12 ARG cc_start: 0.8058 (ptm160) cc_final: 0.7844 (ptp-170) REVERT: E 58 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8601 (mp) REVERT: E 69 ARG cc_start: 0.7861 (ptt180) cc_final: 0.7613 (ptt180) REVERT: E 200 SER cc_start: 0.8856 (p) cc_final: 0.8568 (m) REVERT: E 286 ASP cc_start: 0.8293 (p0) cc_final: 0.8092 (p0) REVERT: E 638 ASP cc_start: 0.7050 (t70) cc_final: 0.6612 (m-30) REVERT: F 32 LYS cc_start: 0.8369 (mtmt) cc_final: 0.7930 (mttm) REVERT: F 36 ASP cc_start: 0.7188 (m-30) cc_final: 0.6748 (m-30) REVERT: G 486 ASN cc_start: 0.8743 (m-40) cc_final: 0.8439 (m-40) REVERT: G 499 ASP cc_start: 0.7817 (m-30) cc_final: 0.7546 (m-30) REVERT: G 638 ASP cc_start: 0.7001 (t70) cc_final: 0.6395 (t70) REVERT: H 17 ASP cc_start: 0.8590 (t0) cc_final: 0.8383 (t70) REVERT: H 111 THR cc_start: 0.8179 (p) cc_final: 0.7913 (t) REVERT: H 116 MET cc_start: 0.8153 (mtt) cc_final: 0.7881 (mtm) outliers start: 12 outliers final: 4 residues processed: 503 average time/residue: 0.4662 time to fit residues: 347.9479 Evaluate side-chains 276 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 270 time to evaluate : 3.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain G residue 309 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 290 optimal weight: 2.9990 chunk 260 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 269 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 312 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 251 GLN A 287 HIS A 480 HIS A 523 GLN A 626 GLN C 403 GLN C 429 HIS C 465 HIS C 695 HIS D 14 ASN E 403 GLN E 429 HIS E 465 HIS E 695 HIS F 14 ASN G 171 GLN G 251 GLN G 287 HIS G 480 HIS G 523 GLN G 626 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28476 Z= 0.175 Angle : 0.566 6.941 38692 Z= 0.307 Chirality : 0.045 0.228 3940 Planarity : 0.006 0.052 5132 Dihedral : 5.798 49.730 3884 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.11 % Allowed : 5.54 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.13), residues: 3440 helix: -0.97 (0.18), residues: 656 sheet: -1.06 (0.20), residues: 716 loop : -1.80 (0.12), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 22 HIS 0.007 0.001 HIS G 465 PHE 0.013 0.002 PHE C 332 TYR 0.015 0.001 TYR G 661 ARG 0.008 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 330 time to evaluate : 2.584 Fit side-chains REVERT: A 177 LYS cc_start: 0.8622 (tttp) cc_final: 0.8384 (tttm) REVERT: A 210 SER cc_start: 0.9163 (p) cc_final: 0.8954 (t) REVERT: A 406 HIS cc_start: 0.7662 (t70) cc_final: 0.7390 (t-170) REVERT: B 116 MET cc_start: 0.8146 (mtt) cc_final: 0.7894 (mtm) REVERT: C 58 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8553 (mp) REVERT: C 200 SER cc_start: 0.8652 (p) cc_final: 0.8387 (m) REVERT: C 343 GLU cc_start: 0.7616 (tt0) cc_final: 0.7367 (tt0) REVERT: D 32 LYS cc_start: 0.8242 (mtmt) cc_final: 0.7926 (mttm) REVERT: D 36 ASP cc_start: 0.7255 (m-30) cc_final: 0.6809 (m-30) REVERT: D 53 PHE cc_start: 0.8972 (m-80) cc_final: 0.8678 (m-80) REVERT: E 58 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8550 (mp) REVERT: E 200 SER cc_start: 0.8650 (p) cc_final: 0.8382 (m) REVERT: E 343 GLU cc_start: 0.7613 (tt0) cc_final: 0.7366 (tt0) REVERT: F 32 LYS cc_start: 0.8241 (mtmt) cc_final: 0.7926 (mttm) REVERT: F 36 ASP cc_start: 0.7253 (m-30) cc_final: 0.6811 (m-30) REVERT: F 53 PHE cc_start: 0.8992 (m-80) cc_final: 0.8710 (m-80) REVERT: G 177 LYS cc_start: 0.8625 (tttp) cc_final: 0.8386 (tttm) REVERT: G 210 SER cc_start: 0.9164 (p) cc_final: 0.8956 (t) REVERT: G 406 HIS cc_start: 0.7641 (t70) cc_final: 0.7373 (t-170) REVERT: H 116 MET cc_start: 0.8151 (mtt) cc_final: 0.7907 (mtm) outliers start: 32 outliers final: 17 residues processed: 355 average time/residue: 0.4135 time to fit residues: 229.3348 Evaluate side-chains 289 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 270 time to evaluate : 3.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 641 GLU Chi-restraints excluded: chain G residue 743 SER Chi-restraints excluded: chain H residue 72 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 173 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 259 optimal weight: 7.9990 chunk 212 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 312 optimal weight: 4.9990 chunk 338 optimal weight: 10.0000 chunk 278 optimal weight: 8.9990 chunk 310 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 251 optimal weight: 9.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 417 HIS A 424 ASN ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 GLN C 28 ASN ** C 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN E 28 ASN E 403 GLN F 14 ASN G 171 GLN G 424 ASN ** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 626 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 28476 Z= 0.616 Angle : 0.739 8.883 38692 Z= 0.392 Chirality : 0.053 0.258 3940 Planarity : 0.007 0.078 5132 Dihedral : 6.019 42.484 3882 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.19 % Allowed : 6.79 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.13), residues: 3440 helix: -0.32 (0.19), residues: 660 sheet: -0.86 (0.19), residues: 752 loop : -1.65 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 331 HIS 0.010 0.002 HIS A 271 PHE 0.035 0.003 PHE E 154 TYR 0.032 0.003 TYR A 661 ARG 0.007 0.001 ARG G 109 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 261 time to evaluate : 3.064 Fit side-chains REVERT: A 294 TYR cc_start: 0.7439 (m-80) cc_final: 0.6978 (m-80) REVERT: A 634 MET cc_start: 0.8516 (mmm) cc_final: 0.7928 (mmm) REVERT: B 17 ASP cc_start: 0.8577 (t0) cc_final: 0.8353 (t70) REVERT: B 116 MET cc_start: 0.8124 (mtt) cc_final: 0.7892 (mtm) REVERT: C 698 MET cc_start: 0.7789 (mmt) cc_final: 0.7364 (mtt) REVERT: D 32 LYS cc_start: 0.8509 (mtmt) cc_final: 0.8017 (mttm) REVERT: D 36 ASP cc_start: 0.7321 (m-30) cc_final: 0.6879 (m-30) REVERT: F 32 LYS cc_start: 0.8506 (mtmt) cc_final: 0.8014 (mttm) REVERT: F 36 ASP cc_start: 0.7321 (m-30) cc_final: 0.6876 (m-30) REVERT: F 53 PHE cc_start: 0.9031 (m-80) cc_final: 0.8761 (m-80) REVERT: F 90 TYR cc_start: 0.8580 (m-80) cc_final: 0.8274 (m-80) REVERT: G 294 TYR cc_start: 0.7435 (m-80) cc_final: 0.6973 (m-80) REVERT: G 634 MET cc_start: 0.8525 (mmm) cc_final: 0.7937 (mmm) REVERT: G 698 MET cc_start: 0.8261 (mmm) cc_final: 0.7956 (mtt) REVERT: H 17 ASP cc_start: 0.8579 (t0) cc_final: 0.8351 (t70) REVERT: H 116 MET cc_start: 0.8160 (mtt) cc_final: 0.7928 (mtm) outliers start: 63 outliers final: 43 residues processed: 317 average time/residue: 0.3793 time to fit residues: 195.0945 Evaluate side-chains 284 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 241 time to evaluate : 3.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 430 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 725 SER Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 518 SER Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 683 VAL Chi-restraints excluded: chain E residue 725 SER Chi-restraints excluded: chain E residue 727 ILE Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 641 GLU Chi-restraints excluded: chain G residue 743 SER Chi-restraints excluded: chain H residue 72 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 309 optimal weight: 0.9980 chunk 235 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 314 optimal weight: 3.9990 chunk 332 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 297 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 417 HIS ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN C 403 GLN D 14 ASN E 403 GLN F 14 ASN G 171 GLN G 417 HIS ** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28476 Z= 0.212 Angle : 0.540 6.725 38692 Z= 0.289 Chirality : 0.045 0.205 3940 Planarity : 0.005 0.052 5132 Dihedral : 5.265 39.777 3878 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.53 % Allowed : 8.15 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.14), residues: 3440 helix: 0.33 (0.20), residues: 660 sheet: -0.78 (0.20), residues: 688 loop : -1.42 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 22 HIS 0.007 0.001 HIS G 465 PHE 0.014 0.002 PHE C 154 TYR 0.016 0.001 TYR G 661 ARG 0.005 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 276 time to evaluate : 3.257 Fit side-chains REVERT: A 294 TYR cc_start: 0.7376 (m-80) cc_final: 0.6923 (m-80) REVERT: A 634 MET cc_start: 0.8455 (mmm) cc_final: 0.7932 (mmm) REVERT: C 622 MET cc_start: 0.9155 (mmp) cc_final: 0.8796 (mmp) REVERT: D 32 LYS cc_start: 0.8485 (mtmt) cc_final: 0.8006 (mttm) REVERT: D 36 ASP cc_start: 0.7293 (m-30) cc_final: 0.6866 (m-30) REVERT: D 53 PHE cc_start: 0.8969 (m-80) cc_final: 0.8703 (m-80) REVERT: F 32 LYS cc_start: 0.8481 (mtmt) cc_final: 0.8002 (mttm) REVERT: F 36 ASP cc_start: 0.7292 (m-30) cc_final: 0.6859 (m-30) REVERT: F 53 PHE cc_start: 0.9013 (m-80) cc_final: 0.8624 (m-80) REVERT: F 90 TYR cc_start: 0.8535 (m-80) cc_final: 0.8280 (m-80) REVERT: G 294 TYR cc_start: 0.7390 (m-80) cc_final: 0.6947 (m-80) REVERT: G 634 MET cc_start: 0.8461 (mmm) cc_final: 0.7863 (mmm) outliers start: 44 outliers final: 30 residues processed: 313 average time/residue: 0.3790 time to fit residues: 192.7948 Evaluate side-chains 285 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 255 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 683 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 417 HIS Chi-restraints excluded: chain G residue 445 ASP Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 689 ASP Chi-restraints excluded: chain H residue 21 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 276 optimal weight: 6.9990 chunk 188 optimal weight: 0.0050 chunk 4 optimal weight: 10.0000 chunk 247 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 283 optimal weight: 0.9990 chunk 229 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN D 14 ASN E 403 GLN F 14 ASN ** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 28476 Z= 0.266 Angle : 0.553 6.786 38692 Z= 0.294 Chirality : 0.046 0.209 3940 Planarity : 0.005 0.052 5132 Dihedral : 5.170 38.869 3878 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.95 % Allowed : 8.15 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.14), residues: 3440 helix: 0.69 (0.21), residues: 636 sheet: -0.65 (0.20), residues: 712 loop : -1.28 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 22 HIS 0.006 0.001 HIS C 695 PHE 0.017 0.002 PHE H 53 TYR 0.018 0.001 TYR G 661 ARG 0.006 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 264 time to evaluate : 3.001 Fit side-chains REVERT: A 294 TYR cc_start: 0.7374 (m-80) cc_final: 0.6907 (m-80) REVERT: A 634 MET cc_start: 0.8510 (mmm) cc_final: 0.7858 (mmm) REVERT: B 53 PHE cc_start: 0.8866 (m-80) cc_final: 0.8534 (m-80) REVERT: C 698 MET cc_start: 0.7855 (mtt) cc_final: 0.7343 (mtt) REVERT: D 32 LYS cc_start: 0.8484 (mtmt) cc_final: 0.8027 (mttm) REVERT: D 36 ASP cc_start: 0.7297 (m-30) cc_final: 0.6895 (m-30) REVERT: D 53 PHE cc_start: 0.8990 (m-80) cc_final: 0.8602 (m-80) REVERT: E 657 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7279 (mm-30) REVERT: F 32 LYS cc_start: 0.8480 (mtmt) cc_final: 0.8024 (mttm) REVERT: F 36 ASP cc_start: 0.7291 (m-30) cc_final: 0.6889 (m-30) REVERT: F 53 PHE cc_start: 0.9022 (m-80) cc_final: 0.8568 (m-80) REVERT: G 294 TYR cc_start: 0.7389 (m-80) cc_final: 0.6930 (m-80) REVERT: G 634 MET cc_start: 0.8520 (mmm) cc_final: 0.7859 (mmm) REVERT: H 53 PHE cc_start: 0.8839 (m-80) cc_final: 0.8507 (m-80) outliers start: 56 outliers final: 47 residues processed: 313 average time/residue: 0.3791 time to fit residues: 192.2287 Evaluate side-chains 301 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 253 time to evaluate : 3.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 516 THR Chi-restraints excluded: chain E residue 518 SER Chi-restraints excluded: chain E residue 657 GLU Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 683 VAL Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 445 ASP Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 641 GLU Chi-restraints excluded: chain G residue 689 ASP Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 130 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 111 optimal weight: 2.9990 chunk 299 optimal weight: 10.0000 chunk 65 optimal weight: 0.5980 chunk 195 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 332 optimal weight: 6.9990 chunk 276 optimal weight: 3.9990 chunk 154 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN G 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 28476 Z= 0.441 Angle : 0.641 10.345 38692 Z= 0.339 Chirality : 0.049 0.227 3940 Planarity : 0.006 0.057 5132 Dihedral : 5.472 42.040 3878 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.26 % Allowed : 8.95 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.14), residues: 3440 helix: 0.59 (0.20), residues: 644 sheet: -0.56 (0.19), residues: 752 loop : -1.33 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 116 HIS 0.008 0.002 HIS A 582 PHE 0.020 0.002 PHE C 154 TYR 0.026 0.002 TYR G 661 ARG 0.006 0.001 ARG C 109 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 245 time to evaluate : 2.928 Fit side-chains REVERT: A 294 TYR cc_start: 0.7390 (m-80) cc_final: 0.6940 (m-80) REVERT: A 634 MET cc_start: 0.8539 (mmm) cc_final: 0.7869 (mmm) REVERT: C 698 MET cc_start: 0.8066 (mtt) cc_final: 0.7665 (mtt) REVERT: D 32 LYS cc_start: 0.8509 (mtmt) cc_final: 0.8039 (mttm) REVERT: D 36 ASP cc_start: 0.7336 (m-30) cc_final: 0.6917 (m-30) REVERT: D 53 PHE cc_start: 0.9014 (m-80) cc_final: 0.8643 (m-80) REVERT: D 75 THR cc_start: 0.7767 (p) cc_final: 0.7564 (t) REVERT: E 657 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7842 (mm-30) REVERT: F 32 LYS cc_start: 0.8508 (mtmt) cc_final: 0.8041 (mttm) REVERT: F 36 ASP cc_start: 0.7331 (m-30) cc_final: 0.6915 (m-30) REVERT: F 53 PHE cc_start: 0.9021 (m-80) cc_final: 0.8609 (m-80) REVERT: F 75 THR cc_start: 0.7787 (p) cc_final: 0.7573 (t) REVERT: G 294 TYR cc_start: 0.7387 (m-80) cc_final: 0.6941 (m-80) REVERT: G 634 MET cc_start: 0.8549 (mmm) cc_final: 0.7873 (mmm) REVERT: H 116 MET cc_start: 0.8072 (mtt) cc_final: 0.7845 (mtm) outliers start: 65 outliers final: 51 residues processed: 305 average time/residue: 0.3774 time to fit residues: 186.6929 Evaluate side-chains 294 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 242 time to evaluate : 3.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 516 THR Chi-restraints excluded: chain E residue 518 SER Chi-restraints excluded: chain E residue 635 GLU Chi-restraints excluded: chain E residue 657 GLU Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 683 VAL Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 641 GLU Chi-restraints excluded: chain G residue 689 ASP Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 130 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 320 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 243 optimal weight: 7.9990 chunk 188 optimal weight: 0.5980 chunk 280 optimal weight: 8.9990 chunk 185 optimal weight: 3.9990 chunk 331 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN F 14 ASN G 171 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28476 Z= 0.219 Angle : 0.536 9.028 38692 Z= 0.285 Chirality : 0.045 0.198 3940 Planarity : 0.005 0.051 5132 Dihedral : 5.077 39.466 3878 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.92 % Allowed : 9.09 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.14), residues: 3440 helix: 0.89 (0.21), residues: 644 sheet: -0.54 (0.19), residues: 716 loop : -1.28 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 22 HIS 0.006 0.001 HIS G 465 PHE 0.012 0.001 PHE B 120 TYR 0.016 0.001 TYR G 661 ARG 0.003 0.000 ARG G 588 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 262 time to evaluate : 3.413 Fit side-chains REVERT: A 294 TYR cc_start: 0.7370 (m-80) cc_final: 0.6912 (m-80) REVERT: A 634 MET cc_start: 0.8534 (mmm) cc_final: 0.7918 (mmm) REVERT: A 698 MET cc_start: 0.8388 (mtp) cc_final: 0.8042 (mtt) REVERT: C 403 GLN cc_start: 0.8446 (mt0) cc_final: 0.8132 (mt0) REVERT: C 698 MET cc_start: 0.7985 (mtt) cc_final: 0.7630 (mtt) REVERT: D 32 LYS cc_start: 0.8498 (mtmt) cc_final: 0.8051 (mttm) REVERT: D 36 ASP cc_start: 0.7302 (m-30) cc_final: 0.6890 (m-30) REVERT: D 53 PHE cc_start: 0.9018 (m-80) cc_final: 0.8599 (m-80) REVERT: D 75 THR cc_start: 0.7773 (p) cc_final: 0.7558 (t) REVERT: E 343 GLU cc_start: 0.7650 (tt0) cc_final: 0.7382 (tt0) REVERT: E 698 MET cc_start: 0.7858 (mtt) cc_final: 0.7448 (mtt) REVERT: F 32 LYS cc_start: 0.8497 (mtmt) cc_final: 0.8052 (mttm) REVERT: F 36 ASP cc_start: 0.7301 (m-30) cc_final: 0.6888 (m-30) REVERT: F 53 PHE cc_start: 0.9013 (m-80) cc_final: 0.8567 (m-80) REVERT: F 75 THR cc_start: 0.7762 (p) cc_final: 0.7555 (t) REVERT: G 294 TYR cc_start: 0.7366 (m-80) cc_final: 0.6908 (m-80) REVERT: G 634 MET cc_start: 0.8539 (mmm) cc_final: 0.7921 (mmm) outliers start: 55 outliers final: 47 residues processed: 312 average time/residue: 0.3808 time to fit residues: 192.9083 Evaluate side-chains 297 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 250 time to evaluate : 3.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 516 THR Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 683 VAL Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 445 ASP Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 585 THR Chi-restraints excluded: chain G residue 689 ASP Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 130 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 205 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 198 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 210 optimal weight: 0.6980 chunk 225 optimal weight: 9.9990 chunk 163 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 260 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 HIS D 14 ASN ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28476 Z= 0.236 Angle : 0.540 8.937 38692 Z= 0.286 Chirality : 0.045 0.206 3940 Planarity : 0.005 0.051 5132 Dihedral : 4.996 37.799 3878 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.02 % Allowed : 9.05 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.14), residues: 3440 helix: 0.98 (0.21), residues: 644 sheet: -0.44 (0.19), residues: 752 loop : -1.20 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 22 HIS 0.005 0.001 HIS F 117 PHE 0.013 0.002 PHE H 120 TYR 0.016 0.001 TYR G 661 ARG 0.003 0.000 ARG G 588 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 254 time to evaluate : 3.335 Fit side-chains REVERT: A 294 TYR cc_start: 0.7367 (m-80) cc_final: 0.6913 (m-80) REVERT: A 634 MET cc_start: 0.8560 (mmm) cc_final: 0.7883 (mmm) REVERT: A 698 MET cc_start: 0.8418 (mtp) cc_final: 0.8091 (mtt) REVERT: B 116 MET cc_start: 0.7955 (mmm) cc_final: 0.7289 (mmm) REVERT: C 698 MET cc_start: 0.7985 (mtt) cc_final: 0.7641 (mtt) REVERT: D 32 LYS cc_start: 0.8485 (mtmt) cc_final: 0.8048 (mttm) REVERT: D 36 ASP cc_start: 0.7304 (m-30) cc_final: 0.6880 (m-30) REVERT: D 53 PHE cc_start: 0.8981 (m-80) cc_final: 0.8519 (m-80) REVERT: D 75 THR cc_start: 0.7772 (p) cc_final: 0.7554 (t) REVERT: E 698 MET cc_start: 0.7929 (mtt) cc_final: 0.7540 (mtt) REVERT: F 32 LYS cc_start: 0.8482 (mtmt) cc_final: 0.8048 (mttm) REVERT: F 36 ASP cc_start: 0.7312 (m-30) cc_final: 0.6891 (m-30) REVERT: F 53 PHE cc_start: 0.9011 (m-80) cc_final: 0.8540 (m-80) REVERT: F 75 THR cc_start: 0.7762 (p) cc_final: 0.7550 (t) REVERT: F 116 MET cc_start: 0.7731 (mtp) cc_final: 0.7342 (mtp) REVERT: G 294 TYR cc_start: 0.7364 (m-80) cc_final: 0.6910 (m-80) REVERT: G 634 MET cc_start: 0.8567 (mmm) cc_final: 0.7885 (mmm) outliers start: 58 outliers final: 50 residues processed: 305 average time/residue: 0.4068 time to fit residues: 200.9497 Evaluate side-chains 298 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 248 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 516 THR Chi-restraints excluded: chain E residue 635 GLU Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 683 VAL Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 417 HIS Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 445 ASP Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 585 THR Chi-restraints excluded: chain G residue 689 ASP Chi-restraints excluded: chain G residue 727 ILE Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 130 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 301 optimal weight: 0.0470 chunk 317 optimal weight: 7.9990 chunk 289 optimal weight: 6.9990 chunk 308 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 242 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 279 optimal weight: 5.9990 chunk 292 optimal weight: 2.9990 chunk 307 optimal weight: 1.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN C 480 HIS ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 HIS ** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28476 Z= 0.179 Angle : 0.514 8.626 38692 Z= 0.272 Chirality : 0.044 0.202 3940 Planarity : 0.004 0.050 5132 Dihedral : 4.770 35.155 3878 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.74 % Allowed : 9.37 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3440 helix: 1.12 (0.21), residues: 644 sheet: -0.47 (0.20), residues: 688 loop : -1.13 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 22 HIS 0.005 0.001 HIS G 465 PHE 0.015 0.001 PHE H 120 TYR 0.015 0.001 TYR C 661 ARG 0.004 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 264 time to evaluate : 3.264 Fit side-chains REVERT: A 294 TYR cc_start: 0.7371 (m-80) cc_final: 0.6944 (m-80) REVERT: A 634 MET cc_start: 0.8460 (mmm) cc_final: 0.7771 (mmm) REVERT: A 698 MET cc_start: 0.8395 (mtp) cc_final: 0.8081 (mtt) REVERT: B 116 MET cc_start: 0.7897 (mmm) cc_final: 0.7340 (mmm) REVERT: C 622 MET cc_start: 0.9111 (mmp) cc_final: 0.8838 (mmp) REVERT: C 698 MET cc_start: 0.8002 (mtt) cc_final: 0.7685 (mtt) REVERT: D 32 LYS cc_start: 0.8468 (mtmt) cc_final: 0.7999 (mttm) REVERT: D 36 ASP cc_start: 0.7289 (m-30) cc_final: 0.6871 (m-30) REVERT: D 53 PHE cc_start: 0.8995 (m-80) cc_final: 0.8523 (m-80) REVERT: D 75 THR cc_start: 0.7743 (p) cc_final: 0.7526 (t) REVERT: D 116 MET cc_start: 0.7759 (mtp) cc_final: 0.7415 (mtp) REVERT: E 698 MET cc_start: 0.7914 (mtt) cc_final: 0.7553 (mtt) REVERT: F 32 LYS cc_start: 0.8468 (mtmt) cc_final: 0.8003 (mttm) REVERT: F 36 ASP cc_start: 0.7294 (m-30) cc_final: 0.6873 (m-30) REVERT: F 53 PHE cc_start: 0.8991 (m-80) cc_final: 0.8491 (m-80) REVERT: F 75 THR cc_start: 0.7751 (p) cc_final: 0.7524 (t) REVERT: F 116 MET cc_start: 0.7785 (mtp) cc_final: 0.7408 (mtp) REVERT: G 294 TYR cc_start: 0.7369 (m-80) cc_final: 0.6910 (m-80) REVERT: G 634 MET cc_start: 0.8465 (mmm) cc_final: 0.7705 (mmm) outliers start: 50 outliers final: 39 residues processed: 308 average time/residue: 0.4005 time to fit residues: 197.7397 Evaluate side-chains 288 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 249 time to evaluate : 3.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 516 THR Chi-restraints excluded: chain E residue 635 GLU Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 683 VAL Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 417 HIS Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 445 ASP Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 585 THR Chi-restraints excluded: chain G residue 689 ASP Chi-restraints excluded: chain H residue 21 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 202 optimal weight: 1.9990 chunk 326 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 154 optimal weight: 9.9990 chunk 227 optimal weight: 0.8980 chunk 342 optimal weight: 7.9990 chunk 315 optimal weight: 2.9990 chunk 272 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 519 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 28476 Z= 0.323 Angle : 0.578 9.006 38692 Z= 0.304 Chirality : 0.047 0.207 3940 Planarity : 0.005 0.059 5132 Dihedral : 5.032 37.557 3878 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.57 % Allowed : 9.89 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3440 helix: 1.04 (0.21), residues: 644 sheet: -0.40 (0.19), residues: 752 loop : -1.13 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 272 HIS 0.005 0.001 HIS G 582 PHE 0.016 0.002 PHE G 187 TYR 0.020 0.001 TYR G 661 ARG 0.004 0.000 ARG C 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 249 time to evaluate : 3.220 Fit side-chains REVERT: A 294 TYR cc_start: 0.7376 (m-80) cc_final: 0.6946 (m-80) REVERT: A 634 MET cc_start: 0.8517 (mmm) cc_final: 0.7778 (mmm) REVERT: B 116 MET cc_start: 0.7878 (mmm) cc_final: 0.7257 (mmm) REVERT: C 698 MET cc_start: 0.8036 (mtt) cc_final: 0.7711 (mtt) REVERT: D 32 LYS cc_start: 0.8491 (mtmt) cc_final: 0.8059 (mttm) REVERT: D 36 ASP cc_start: 0.7314 (m-30) cc_final: 0.6892 (m-30) REVERT: D 53 PHE cc_start: 0.9016 (m-80) cc_final: 0.8551 (m-80) REVERT: D 75 THR cc_start: 0.7739 (p) cc_final: 0.7534 (t) REVERT: E 698 MET cc_start: 0.8004 (mtt) cc_final: 0.7656 (mtt) REVERT: F 32 LYS cc_start: 0.8491 (mtmt) cc_final: 0.8063 (mttm) REVERT: F 36 ASP cc_start: 0.7322 (m-30) cc_final: 0.6898 (m-30) REVERT: F 53 PHE cc_start: 0.9005 (m-80) cc_final: 0.8510 (m-80) REVERT: F 75 THR cc_start: 0.7740 (p) cc_final: 0.7535 (t) REVERT: F 116 MET cc_start: 0.7826 (mtp) cc_final: 0.7440 (mtp) REVERT: G 294 TYR cc_start: 0.7371 (m-80) cc_final: 0.6945 (m-80) REVERT: G 634 MET cc_start: 0.8526 (mmm) cc_final: 0.7778 (mmm) REVERT: H 116 MET cc_start: 0.8247 (mtm) cc_final: 0.7789 (mtp) outliers start: 45 outliers final: 39 residues processed: 289 average time/residue: 0.3906 time to fit residues: 181.1952 Evaluate side-chains 286 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 247 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 516 THR Chi-restraints excluded: chain E residue 635 GLU Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 683 VAL Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 417 HIS Chi-restraints excluded: chain G residue 420 VAL Chi-restraints excluded: chain G residue 513 VAL Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 585 THR Chi-restraints excluded: chain G residue 689 ASP Chi-restraints excluded: chain H residue 21 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 216 optimal weight: 0.9990 chunk 290 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 251 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 273 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 280 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 519 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.112850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.089315 restraints weight = 38158.727| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.66 r_work: 0.2825 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28476 Z= 0.201 Angle : 0.532 10.567 38692 Z= 0.279 Chirality : 0.045 0.200 3940 Planarity : 0.004 0.051 5132 Dihedral : 4.842 36.461 3878 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.57 % Allowed : 9.99 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 3440 helix: 1.18 (0.21), residues: 644 sheet: -0.26 (0.19), residues: 728 loop : -1.09 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 22 HIS 0.005 0.001 HIS G 465 PHE 0.011 0.001 PHE H 120 TYR 0.015 0.001 TYR E 661 ARG 0.003 0.000 ARG A 588 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5533.66 seconds wall clock time: 101 minutes 11.88 seconds (6071.88 seconds total)