Starting phenix.real_space_refine on Tue Sep 24 06:35:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sya_25521/09_2024/7sya_25521.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sya_25521/09_2024/7sya_25521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sya_25521/09_2024/7sya_25521.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sya_25521/09_2024/7sya_25521.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sya_25521/09_2024/7sya_25521.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sya_25521/09_2024/7sya_25521.cif" } resolution = 3.5 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= 0.002 sd= 0.007 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 288 5.16 5 C 31284 2.51 5 N 8736 2.21 5 O 9552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.61s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 49860 Number of models: 1 Model: "" Number of chains: 12 Chain: "a" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4155 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 15, 'TRANS': 499} Chain breaks: 2 Chain: "b" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4155 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 15, 'TRANS': 499} Chain breaks: 2 Chain: "c" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4155 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 15, 'TRANS': 499} Chain breaks: 2 Chain: "d" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4155 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 15, 'TRANS': 499} Chain breaks: 2 Chain: "e" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4155 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 15, 'TRANS': 499} Chain breaks: 2 Chain: "f" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4155 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 15, 'TRANS': 499} Chain breaks: 2 Chain: "g" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4155 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 15, 'TRANS': 499} Chain breaks: 2 Chain: "h" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4155 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 15, 'TRANS': 499} Chain breaks: 2 Chain: "i" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4155 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 15, 'TRANS': 499} Chain breaks: 2 Chain: "j" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4155 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 15, 'TRANS': 499} Chain breaks: 2 Chain: "k" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4155 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 15, 'TRANS': 499} Chain breaks: 2 Chain: "l" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4155 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 15, 'TRANS': 499} Chain breaks: 2 Time building chain proxies: 22.67, per 1000 atoms: 0.45 Number of scatterers: 49860 At special positions: 0 Unit cell: (192.01, 192.01, 134.68, 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 288 16.00 O 9552 8.00 N 8736 7.00 C 31284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.03 Conformation dependent library (CDL) restraints added in 4.5 seconds 12216 Ramachandran restraints generated. 6108 Oldfield, 0 Emsley, 6108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11616 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 28 sheets defined 48.9% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'a' and resid 13 through 46 Processing helix chain 'a' and resid 64 through 81 removed outlier: 3.777A pdb=" N THR a 68 " --> pdb=" O ASP a 64 " (cutoff:3.500A) Proline residue: a 74 - end of helix Processing helix chain 'a' and resid 99 through 112 Processing helix chain 'a' and resid 118 through 131 Processing helix chain 'a' and resid 200 through 204 Processing helix chain 'a' and resid 212 through 216 removed outlier: 3.551A pdb=" N ASP a 215 " --> pdb=" O CYS a 212 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA a 216 " --> pdb=" O ILE a 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 212 through 216' Processing helix chain 'a' and resid 226 through 234 Processing helix chain 'a' and resid 339 through 368 removed outlier: 3.574A pdb=" N LYS a 343 " --> pdb=" O SER a 339 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASP a 346 " --> pdb=" O ASP a 342 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ILE a 347 " --> pdb=" O LYS a 343 " (cutoff:3.500A) Processing helix chain 'a' and resid 379 through 385 removed outlier: 3.935A pdb=" N ASN a 385 " --> pdb=" O LEU a 382 " (cutoff:3.500A) Processing helix chain 'a' and resid 409 through 426 removed outlier: 3.751A pdb=" N GLY a 413 " --> pdb=" O GLY a 409 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR a 426 " --> pdb=" O ARG a 422 " (cutoff:3.500A) Processing helix chain 'a' and resid 445 through 458 Processing helix chain 'a' and resid 458 through 485 removed outlier: 3.867A pdb=" N LEU a 462 " --> pdb=" O GLN a 458 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS a 473 " --> pdb=" O GLU a 469 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG a 474 " --> pdb=" O THR a 470 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS a 485 " --> pdb=" O ASP a 481 " (cutoff:3.500A) Processing helix chain 'a' and resid 522 through 545 removed outlier: 3.514A pdb=" N MET a 528 " --> pdb=" O LYS a 524 " (cutoff:3.500A) Processing helix chain 'a' and resid 552 through 566 removed outlier: 3.562A pdb=" N ASN a 558 " --> pdb=" O GLN a 554 " (cutoff:3.500A) Processing helix chain 'a' and resid 581 through 590 removed outlier: 3.662A pdb=" N GLN a 586 " --> pdb=" O PRO a 582 " (cutoff:3.500A) Processing helix chain 'a' and resid 590 through 595 removed outlier: 3.531A pdb=" N GLU a 595 " --> pdb=" O ARG a 591 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 46 Processing helix chain 'b' and resid 64 through 81 removed outlier: 3.831A pdb=" N THR b 68 " --> pdb=" O ASP b 64 " (cutoff:3.500A) Proline residue: b 74 - end of helix Processing helix chain 'b' and resid 99 through 112 Processing helix chain 'b' and resid 118 through 131 Processing helix chain 'b' and resid 200 through 204 Processing helix chain 'b' and resid 212 through 216 removed outlier: 3.557A pdb=" N ASP b 215 " --> pdb=" O CYS b 212 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA b 216 " --> pdb=" O ILE b 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 212 through 216' Processing helix chain 'b' and resid 226 through 234 Processing helix chain 'b' and resid 339 through 368 removed outlier: 3.578A pdb=" N LYS b 343 " --> pdb=" O SER b 339 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASP b 346 " --> pdb=" O ASP b 342 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE b 347 " --> pdb=" O LYS b 343 " (cutoff:3.500A) Processing helix chain 'b' and resid 379 through 385 removed outlier: 3.976A pdb=" N ASN b 385 " --> pdb=" O LEU b 382 " (cutoff:3.500A) Processing helix chain 'b' and resid 409 through 426 removed outlier: 3.811A pdb=" N GLY b 413 " --> pdb=" O GLY b 409 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR b 426 " --> pdb=" O ARG b 422 " (cutoff:3.500A) Processing helix chain 'b' and resid 445 through 458 Processing helix chain 'b' and resid 458 through 485 removed outlier: 3.878A pdb=" N LEU b 462 " --> pdb=" O GLN b 458 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LYS b 473 " --> pdb=" O GLU b 469 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG b 474 " --> pdb=" O THR b 470 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LYS b 485 " --> pdb=" O ASP b 481 " (cutoff:3.500A) Processing helix chain 'b' and resid 522 through 545 removed outlier: 3.553A pdb=" N MET b 528 " --> pdb=" O LYS b 524 " (cutoff:3.500A) Processing helix chain 'b' and resid 552 through 566 Processing helix chain 'b' and resid 581 through 590 Processing helix chain 'b' and resid 590 through 595 removed outlier: 3.513A pdb=" N GLU b 595 " --> pdb=" O ARG b 591 " (cutoff:3.500A) Processing helix chain 'c' and resid 13 through 46 Processing helix chain 'c' and resid 64 through 81 removed outlier: 3.916A pdb=" N THR c 68 " --> pdb=" O ASP c 64 " (cutoff:3.500A) Proline residue: c 74 - end of helix Processing helix chain 'c' and resid 99 through 112 Processing helix chain 'c' and resid 118 through 131 Processing helix chain 'c' and resid 200 through 204 Processing helix chain 'c' and resid 212 through 216 removed outlier: 3.597A pdb=" N ASP c 215 " --> pdb=" O CYS c 212 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA c 216 " --> pdb=" O ILE c 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 212 through 216' Processing helix chain 'c' and resid 226 through 234 Processing helix chain 'c' and resid 339 through 368 removed outlier: 3.599A pdb=" N LYS c 343 " --> pdb=" O SER c 339 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ASP c 346 " --> pdb=" O ASP c 342 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ILE c 347 " --> pdb=" O LYS c 343 " (cutoff:3.500A) Processing helix chain 'c' and resid 379 through 385 removed outlier: 3.950A pdb=" N ASN c 385 " --> pdb=" O LEU c 382 " (cutoff:3.500A) Processing helix chain 'c' and resid 409 through 426 removed outlier: 3.743A pdb=" N GLY c 413 " --> pdb=" O GLY c 409 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR c 426 " --> pdb=" O ARG c 422 " (cutoff:3.500A) Processing helix chain 'c' and resid 445 through 458 Processing helix chain 'c' and resid 458 through 485 removed outlier: 3.917A pdb=" N LEU c 462 " --> pdb=" O GLN c 458 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS c 473 " --> pdb=" O GLU c 469 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG c 474 " --> pdb=" O THR c 470 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS c 485 " --> pdb=" O ASP c 481 " (cutoff:3.500A) Processing helix chain 'c' and resid 522 through 545 removed outlier: 3.631A pdb=" N MET c 528 " --> pdb=" O LYS c 524 " (cutoff:3.500A) Processing helix chain 'c' and resid 552 through 566 Processing helix chain 'c' and resid 581 through 590 removed outlier: 3.721A pdb=" N GLN c 586 " --> pdb=" O PRO c 582 " (cutoff:3.500A) Processing helix chain 'c' and resid 590 through 595 removed outlier: 3.552A pdb=" N GLU c 595 " --> pdb=" O ARG c 591 " (cutoff:3.500A) Processing helix chain 'd' and resid 13 through 46 Processing helix chain 'd' and resid 64 through 81 removed outlier: 3.726A pdb=" N THR d 68 " --> pdb=" O ASP d 64 " (cutoff:3.500A) Proline residue: d 74 - end of helix Processing helix chain 'd' and resid 99 through 112 Processing helix chain 'd' and resid 118 through 131 Processing helix chain 'd' and resid 200 through 204 Processing helix chain 'd' and resid 212 through 216 removed outlier: 3.578A pdb=" N ASP d 215 " --> pdb=" O CYS d 212 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA d 216 " --> pdb=" O ILE d 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 212 through 216' Processing helix chain 'd' and resid 226 through 234 Processing helix chain 'd' and resid 339 through 368 removed outlier: 3.590A pdb=" N LYS d 343 " --> pdb=" O SER d 339 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASP d 346 " --> pdb=" O ASP d 342 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE d 347 " --> pdb=" O LYS d 343 " (cutoff:3.500A) Processing helix chain 'd' and resid 379 through 385 removed outlier: 3.955A pdb=" N ASN d 385 " --> pdb=" O LEU d 382 " (cutoff:3.500A) Processing helix chain 'd' and resid 409 through 426 removed outlier: 3.644A pdb=" N GLY d 413 " --> pdb=" O GLY d 409 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR d 426 " --> pdb=" O ARG d 422 " (cutoff:3.500A) Processing helix chain 'd' and resid 445 through 458 removed outlier: 3.513A pdb=" N GLN d 458 " --> pdb=" O THR d 454 " (cutoff:3.500A) Processing helix chain 'd' and resid 458 through 484 removed outlier: 3.883A pdb=" N LEU d 462 " --> pdb=" O GLN d 458 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LYS d 473 " --> pdb=" O GLU d 469 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG d 474 " --> pdb=" O THR d 470 " (cutoff:3.500A) Processing helix chain 'd' and resid 522 through 545 removed outlier: 3.875A pdb=" N MET d 528 " --> pdb=" O LYS d 524 " (cutoff:3.500A) Processing helix chain 'd' and resid 552 through 566 Processing helix chain 'd' and resid 581 through 590 removed outlier: 3.531A pdb=" N ILE d 590 " --> pdb=" O GLN d 586 " (cutoff:3.500A) Processing helix chain 'd' and resid 590 through 595 Processing helix chain 'e' and resid 13 through 46 Processing helix chain 'e' and resid 64 through 81 removed outlier: 3.779A pdb=" N THR e 68 " --> pdb=" O ASP e 64 " (cutoff:3.500A) Proline residue: e 74 - end of helix Processing helix chain 'e' and resid 99 through 112 Processing helix chain 'e' and resid 118 through 131 Processing helix chain 'e' and resid 200 through 204 Processing helix chain 'e' and resid 212 through 216 removed outlier: 3.555A pdb=" N ASP e 215 " --> pdb=" O CYS e 212 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA e 216 " --> pdb=" O ILE e 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 212 through 216' Processing helix chain 'e' and resid 226 through 234 Processing helix chain 'e' and resid 339 through 368 removed outlier: 3.610A pdb=" N LYS e 343 " --> pdb=" O SER e 339 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ASP e 346 " --> pdb=" O ASP e 342 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ILE e 347 " --> pdb=" O LYS e 343 " (cutoff:3.500A) Processing helix chain 'e' and resid 379 through 385 removed outlier: 3.932A pdb=" N ASN e 385 " --> pdb=" O LEU e 382 " (cutoff:3.500A) Processing helix chain 'e' and resid 409 through 426 removed outlier: 3.707A pdb=" N GLY e 413 " --> pdb=" O GLY e 409 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR e 426 " --> pdb=" O ARG e 422 " (cutoff:3.500A) Processing helix chain 'e' and resid 445 through 458 Processing helix chain 'e' and resid 458 through 485 removed outlier: 3.874A pdb=" N LEU e 462 " --> pdb=" O GLN e 458 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS e 473 " --> pdb=" O GLU e 469 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG e 474 " --> pdb=" O THR e 470 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS e 485 " --> pdb=" O ASP e 481 " (cutoff:3.500A) Processing helix chain 'e' and resid 522 through 545 Processing helix chain 'e' and resid 552 through 568 removed outlier: 3.625A pdb=" N ASN e 558 " --> pdb=" O GLN e 554 " (cutoff:3.500A) Processing helix chain 'e' and resid 581 through 590 removed outlier: 3.668A pdb=" N GLN e 586 " --> pdb=" O PRO e 582 " (cutoff:3.500A) Processing helix chain 'e' and resid 590 through 595 removed outlier: 3.519A pdb=" N GLU e 595 " --> pdb=" O ARG e 591 " (cutoff:3.500A) Processing helix chain 'f' and resid 13 through 46 Processing helix chain 'f' and resid 64 through 81 removed outlier: 3.881A pdb=" N THR f 68 " --> pdb=" O ASP f 64 " (cutoff:3.500A) Proline residue: f 74 - end of helix Processing helix chain 'f' and resid 99 through 112 Processing helix chain 'f' and resid 118 through 131 Processing helix chain 'f' and resid 200 through 204 Processing helix chain 'f' and resid 212 through 216 removed outlier: 3.558A pdb=" N ASP f 215 " --> pdb=" O CYS f 212 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA f 216 " --> pdb=" O ILE f 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 212 through 216' Processing helix chain 'f' and resid 226 through 234 Processing helix chain 'f' and resid 339 through 368 removed outlier: 3.598A pdb=" N LYS f 343 " --> pdb=" O SER f 339 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASP f 346 " --> pdb=" O ASP f 342 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ILE f 347 " --> pdb=" O LYS f 343 " (cutoff:3.500A) Processing helix chain 'f' and resid 379 through 385 removed outlier: 3.902A pdb=" N ASN f 385 " --> pdb=" O LEU f 382 " (cutoff:3.500A) Processing helix chain 'f' and resid 409 through 426 removed outlier: 3.612A pdb=" N GLY f 413 " --> pdb=" O GLY f 409 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR f 426 " --> pdb=" O ARG f 422 " (cutoff:3.500A) Processing helix chain 'f' and resid 445 through 458 Processing helix chain 'f' and resid 458 through 485 removed outlier: 3.851A pdb=" N LEU f 462 " --> pdb=" O GLN f 458 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS f 473 " --> pdb=" O GLU f 469 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG f 474 " --> pdb=" O THR f 470 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS f 485 " --> pdb=" O ASP f 481 " (cutoff:3.500A) Processing helix chain 'f' and resid 522 through 545 Processing helix chain 'f' and resid 552 through 566 removed outlier: 3.588A pdb=" N ASN f 558 " --> pdb=" O GLN f 554 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN f 566 " --> pdb=" O GLU f 562 " (cutoff:3.500A) Processing helix chain 'f' and resid 581 through 590 removed outlier: 3.725A pdb=" N GLN f 586 " --> pdb=" O PRO f 582 " (cutoff:3.500A) Processing helix chain 'f' and resid 590 through 595 removed outlier: 3.539A pdb=" N GLU f 595 " --> pdb=" O ARG f 591 " (cutoff:3.500A) Processing helix chain 'g' and resid 13 through 46 Processing helix chain 'g' and resid 64 through 81 Proline residue: g 74 - end of helix Processing helix chain 'g' and resid 99 through 112 Processing helix chain 'g' and resid 118 through 131 Processing helix chain 'g' and resid 200 through 204 Processing helix chain 'g' and resid 212 through 216 removed outlier: 3.562A pdb=" N ASP g 215 " --> pdb=" O CYS g 212 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA g 216 " --> pdb=" O ILE g 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 212 through 216' Processing helix chain 'g' and resid 226 through 234 Processing helix chain 'g' and resid 339 through 368 removed outlier: 3.631A pdb=" N LYS g 343 " --> pdb=" O SER g 339 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASP g 346 " --> pdb=" O ASP g 342 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE g 347 " --> pdb=" O LYS g 343 " (cutoff:3.500A) Processing helix chain 'g' and resid 379 through 385 removed outlier: 3.912A pdb=" N ASN g 385 " --> pdb=" O LEU g 382 " (cutoff:3.500A) Processing helix chain 'g' and resid 408 through 426 removed outlier: 4.163A pdb=" N TYR g 412 " --> pdb=" O SER g 408 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR g 426 " --> pdb=" O ARG g 422 " (cutoff:3.500A) Processing helix chain 'g' and resid 445 through 458 Processing helix chain 'g' and resid 458 through 485 removed outlier: 3.792A pdb=" N LEU g 462 " --> pdb=" O GLN g 458 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS g 473 " --> pdb=" O GLU g 469 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG g 474 " --> pdb=" O THR g 470 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS g 485 " --> pdb=" O ASP g 481 " (cutoff:3.500A) Processing helix chain 'g' and resid 522 through 545 Processing helix chain 'g' and resid 552 through 568 Processing helix chain 'g' and resid 581 through 590 removed outlier: 4.047A pdb=" N GLN g 586 " --> pdb=" O PRO g 582 " (cutoff:3.500A) Processing helix chain 'h' and resid 13 through 46 Processing helix chain 'h' and resid 64 through 81 Proline residue: h 74 - end of helix Processing helix chain 'h' and resid 99 through 112 Processing helix chain 'h' and resid 118 through 131 Processing helix chain 'h' and resid 200 through 204 Processing helix chain 'h' and resid 212 through 216 removed outlier: 3.560A pdb=" N ASP h 215 " --> pdb=" O CYS h 212 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA h 216 " --> pdb=" O ILE h 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 212 through 216' Processing helix chain 'h' and resid 226 through 234 Processing helix chain 'h' and resid 339 through 368 removed outlier: 3.617A pdb=" N LYS h 343 " --> pdb=" O SER h 339 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP h 346 " --> pdb=" O ASP h 342 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ILE h 347 " --> pdb=" O LYS h 343 " (cutoff:3.500A) Processing helix chain 'h' and resid 379 through 385 removed outlier: 3.891A pdb=" N ASN h 385 " --> pdb=" O LEU h 382 " (cutoff:3.500A) Processing helix chain 'h' and resid 409 through 426 removed outlier: 3.676A pdb=" N GLY h 413 " --> pdb=" O GLY h 409 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU h 418 " --> pdb=" O MET h 414 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR h 426 " --> pdb=" O ARG h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 445 through 458 Processing helix chain 'h' and resid 458 through 485 removed outlier: 3.788A pdb=" N LEU h 462 " --> pdb=" O GLN h 458 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS h 473 " --> pdb=" O GLU h 469 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG h 474 " --> pdb=" O THR h 470 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LYS h 485 " --> pdb=" O ASP h 481 " (cutoff:3.500A) Processing helix chain 'h' and resid 512 through 516 removed outlier: 3.641A pdb=" N VAL h 515 " --> pdb=" O ASP h 512 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR h 516 " --> pdb=" O LEU h 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 512 through 516' Processing helix chain 'h' and resid 522 through 545 Processing helix chain 'h' and resid 552 through 566 removed outlier: 3.518A pdb=" N ASN h 558 " --> pdb=" O GLN h 554 " (cutoff:3.500A) Processing helix chain 'h' and resid 581 through 590 removed outlier: 3.831A pdb=" N GLN h 586 " --> pdb=" O PRO h 582 " (cutoff:3.500A) Processing helix chain 'h' and resid 590 through 595 removed outlier: 3.502A pdb=" N GLU h 595 " --> pdb=" O ARG h 591 " (cutoff:3.500A) Processing helix chain 'i' and resid 13 through 46 Processing helix chain 'i' and resid 64 through 81 removed outlier: 3.739A pdb=" N THR i 68 " --> pdb=" O ASP i 64 " (cutoff:3.500A) Proline residue: i 74 - end of helix Processing helix chain 'i' and resid 99 through 112 Processing helix chain 'i' and resid 118 through 131 Processing helix chain 'i' and resid 200 through 204 Processing helix chain 'i' and resid 212 through 216 removed outlier: 3.581A pdb=" N ASP i 215 " --> pdb=" O CYS i 212 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA i 216 " --> pdb=" O ILE i 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 212 through 216' Processing helix chain 'i' and resid 226 through 234 Processing helix chain 'i' and resid 339 through 368 removed outlier: 3.571A pdb=" N LYS i 343 " --> pdb=" O SER i 339 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASP i 346 " --> pdb=" O ASP i 342 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ILE i 347 " --> pdb=" O LYS i 343 " (cutoff:3.500A) Processing helix chain 'i' and resid 379 through 385 removed outlier: 3.953A pdb=" N ASN i 385 " --> pdb=" O LEU i 382 " (cutoff:3.500A) Processing helix chain 'i' and resid 409 through 426 removed outlier: 3.628A pdb=" N GLY i 413 " --> pdb=" O GLY i 409 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR i 426 " --> pdb=" O ARG i 422 " (cutoff:3.500A) Processing helix chain 'i' and resid 445 through 458 removed outlier: 3.567A pdb=" N GLN i 458 " --> pdb=" O THR i 454 " (cutoff:3.500A) Processing helix chain 'i' and resid 458 through 485 removed outlier: 3.900A pdb=" N LEU i 462 " --> pdb=" O GLN i 458 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS i 473 " --> pdb=" O GLU i 469 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG i 474 " --> pdb=" O THR i 470 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS i 485 " --> pdb=" O ASP i 481 " (cutoff:3.500A) Processing helix chain 'i' and resid 522 through 545 removed outlier: 3.963A pdb=" N MET i 528 " --> pdb=" O LYS i 524 " (cutoff:3.500A) Processing helix chain 'i' and resid 552 through 566 removed outlier: 3.664A pdb=" N ASN i 558 " --> pdb=" O GLN i 554 " (cutoff:3.500A) Processing helix chain 'i' and resid 581 through 590 removed outlier: 3.535A pdb=" N ILE i 590 " --> pdb=" O GLN i 586 " (cutoff:3.500A) Processing helix chain 'i' and resid 590 through 595 Processing helix chain 'j' and resid 13 through 46 Processing helix chain 'j' and resid 64 through 81 removed outlier: 3.752A pdb=" N THR j 68 " --> pdb=" O ASP j 64 " (cutoff:3.500A) Proline residue: j 74 - end of helix Processing helix chain 'j' and resid 99 through 112 Processing helix chain 'j' and resid 118 through 131 Processing helix chain 'j' and resid 200 through 204 Processing helix chain 'j' and resid 212 through 216 removed outlier: 3.564A pdb=" N ASP j 215 " --> pdb=" O CYS j 212 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA j 216 " --> pdb=" O ILE j 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 212 through 216' Processing helix chain 'j' and resid 226 through 234 Processing helix chain 'j' and resid 339 through 368 removed outlier: 3.585A pdb=" N LYS j 343 " --> pdb=" O SER j 339 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASP j 346 " --> pdb=" O ASP j 342 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE j 347 " --> pdb=" O LYS j 343 " (cutoff:3.500A) Processing helix chain 'j' and resid 379 through 385 removed outlier: 3.941A pdb=" N ASN j 385 " --> pdb=" O LEU j 382 " (cutoff:3.500A) Processing helix chain 'j' and resid 409 through 426 removed outlier: 3.625A pdb=" N GLY j 413 " --> pdb=" O GLY j 409 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR j 426 " --> pdb=" O ARG j 422 " (cutoff:3.500A) Processing helix chain 'j' and resid 445 through 458 removed outlier: 3.531A pdb=" N GLN j 458 " --> pdb=" O THR j 454 " (cutoff:3.500A) Processing helix chain 'j' and resid 458 through 485 removed outlier: 3.896A pdb=" N LEU j 462 " --> pdb=" O GLN j 458 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LYS j 473 " --> pdb=" O GLU j 469 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG j 474 " --> pdb=" O THR j 470 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS j 485 " --> pdb=" O ASP j 481 " (cutoff:3.500A) Processing helix chain 'j' and resid 522 through 545 removed outlier: 3.964A pdb=" N MET j 528 " --> pdb=" O LYS j 524 " (cutoff:3.500A) Processing helix chain 'j' and resid 552 through 568 removed outlier: 3.671A pdb=" N ASN j 558 " --> pdb=" O GLN j 554 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL j 563 " --> pdb=" O ILE j 559 " (cutoff:3.500A) Processing helix chain 'j' and resid 581 through 590 removed outlier: 3.549A pdb=" N ILE j 590 " --> pdb=" O GLN j 586 " (cutoff:3.500A) Processing helix chain 'j' and resid 590 through 595 Processing helix chain 'k' and resid 13 through 46 Processing helix chain 'k' and resid 64 through 81 Proline residue: k 74 - end of helix Processing helix chain 'k' and resid 99 through 112 Processing helix chain 'k' and resid 118 through 131 Processing helix chain 'k' and resid 200 through 204 Processing helix chain 'k' and resid 212 through 216 removed outlier: 3.585A pdb=" N ASP k 215 " --> pdb=" O CYS k 212 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA k 216 " --> pdb=" O ILE k 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 212 through 216' Processing helix chain 'k' and resid 226 through 234 Processing helix chain 'k' and resid 339 through 368 removed outlier: 3.642A pdb=" N LYS k 343 " --> pdb=" O SER k 339 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASP k 346 " --> pdb=" O ASP k 342 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ILE k 347 " --> pdb=" O LYS k 343 " (cutoff:3.500A) Processing helix chain 'k' and resid 379 through 385 removed outlier: 3.908A pdb=" N ASN k 385 " --> pdb=" O LEU k 382 " (cutoff:3.500A) Processing helix chain 'k' and resid 409 through 426 removed outlier: 3.830A pdb=" N THR k 426 " --> pdb=" O ARG k 422 " (cutoff:3.500A) Processing helix chain 'k' and resid 445 through 458 Processing helix chain 'k' and resid 458 through 485 removed outlier: 3.812A pdb=" N LEU k 462 " --> pdb=" O GLN k 458 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS k 473 " --> pdb=" O GLU k 469 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG k 474 " --> pdb=" O THR k 470 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS k 485 " --> pdb=" O ASP k 481 " (cutoff:3.500A) Processing helix chain 'k' and resid 522 through 545 Processing helix chain 'k' and resid 552 through 566 Processing helix chain 'k' and resid 581 through 590 removed outlier: 3.806A pdb=" N GLN k 586 " --> pdb=" O PRO k 582 " (cutoff:3.500A) Processing helix chain 'k' and resid 590 through 595 removed outlier: 3.505A pdb=" N GLU k 595 " --> pdb=" O ARG k 591 " (cutoff:3.500A) Processing helix chain 'l' and resid 13 through 46 Processing helix chain 'l' and resid 64 through 81 removed outlier: 3.803A pdb=" N THR l 68 " --> pdb=" O ASP l 64 " (cutoff:3.500A) Proline residue: l 74 - end of helix Processing helix chain 'l' and resid 99 through 112 Processing helix chain 'l' and resid 118 through 131 Processing helix chain 'l' and resid 200 through 204 Processing helix chain 'l' and resid 212 through 216 removed outlier: 3.600A pdb=" N ASP l 215 " --> pdb=" O CYS l 212 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA l 216 " --> pdb=" O ILE l 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 212 through 216' Processing helix chain 'l' and resid 226 through 234 Processing helix chain 'l' and resid 339 through 368 removed outlier: 3.599A pdb=" N LYS l 343 " --> pdb=" O SER l 339 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASP l 346 " --> pdb=" O ASP l 342 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ILE l 347 " --> pdb=" O LYS l 343 " (cutoff:3.500A) Processing helix chain 'l' and resid 379 through 385 removed outlier: 3.911A pdb=" N ASN l 385 " --> pdb=" O LEU l 382 " (cutoff:3.500A) Processing helix chain 'l' and resid 408 through 426 removed outlier: 4.223A pdb=" N TYR l 412 " --> pdb=" O SER l 408 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR l 426 " --> pdb=" O ARG l 422 " (cutoff:3.500A) Processing helix chain 'l' and resid 445 through 458 removed outlier: 3.598A pdb=" N VAL l 449 " --> pdb=" O ALA l 445 " (cutoff:3.500A) Processing helix chain 'l' and resid 458 through 485 removed outlier: 3.923A pdb=" N LEU l 462 " --> pdb=" O GLN l 458 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LYS l 473 " --> pdb=" O GLU l 469 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG l 474 " --> pdb=" O THR l 470 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS l 485 " --> pdb=" O ASP l 481 " (cutoff:3.500A) Processing helix chain 'l' and resid 522 through 545 Processing helix chain 'l' and resid 552 through 568 Processing helix chain 'l' and resid 581 through 590 removed outlier: 3.663A pdb=" N GLN l 586 " --> pdb=" O PRO l 582 " (cutoff:3.500A) Processing helix chain 'l' and resid 590 through 595 removed outlier: 3.562A pdb=" N GLU l 595 " --> pdb=" O ARG l 591 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 136 through 140 Processing sheet with id=AA2, first strand: chain 'a' and resid 143 through 144 Processing sheet with id=AA3, first strand: chain 'a' and resid 218 through 223 Processing sheet with id=AA4, first strand: chain 'b' and resid 136 through 140 Processing sheet with id=AA5, first strand: chain 'b' and resid 218 through 223 Processing sheet with id=AA6, first strand: chain 'c' and resid 136 through 140 Processing sheet with id=AA7, first strand: chain 'c' and resid 218 through 223 Processing sheet with id=AA8, first strand: chain 'd' and resid 136 through 140 Processing sheet with id=AA9, first strand: chain 'd' and resid 143 through 144 Processing sheet with id=AB1, first strand: chain 'd' and resid 218 through 223 Processing sheet with id=AB2, first strand: chain 'e' and resid 136 through 140 Processing sheet with id=AB3, first strand: chain 'e' and resid 218 through 223 Processing sheet with id=AB4, first strand: chain 'f' and resid 136 through 140 Processing sheet with id=AB5, first strand: chain 'f' and resid 218 through 223 Processing sheet with id=AB6, first strand: chain 'g' and resid 136 through 143 Processing sheet with id=AB7, first strand: chain 'g' and resid 218 through 223 Processing sheet with id=AB8, first strand: chain 'h' and resid 136 through 140 Processing sheet with id=AB9, first strand: chain 'h' and resid 218 through 223 Processing sheet with id=AC1, first strand: chain 'i' and resid 136 through 140 Processing sheet with id=AC2, first strand: chain 'i' and resid 143 through 144 Processing sheet with id=AC3, first strand: chain 'i' and resid 218 through 223 Processing sheet with id=AC4, first strand: chain 'j' and resid 136 through 140 Processing sheet with id=AC5, first strand: chain 'j' and resid 143 through 144 Processing sheet with id=AC6, first strand: chain 'j' and resid 218 through 223 Processing sheet with id=AC7, first strand: chain 'k' and resid 136 through 140 Processing sheet with id=AC8, first strand: chain 'k' and resid 218 through 223 Processing sheet with id=AC9, first strand: chain 'l' and resid 136 through 140 Processing sheet with id=AD1, first strand: chain 'l' and resid 218 through 223 2266 hydrogen bonds defined for protein. 6543 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: 12.62 Time building geometry restraints manager: 10.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 16906 1.34 - 1.46: 8604 1.46 - 1.58: 24686 1.58 - 1.70: 0 1.70 - 1.82: 516 Bond restraints: 50712 Sorted by residual: bond pdb=" C ASN a 580 " pdb=" N SER a 581 " ideal model delta sigma weight residual 1.330 1.366 -0.036 1.47e-02 4.63e+03 5.94e+00 bond pdb=" CG GLU i 536 " pdb=" CD GLU i 536 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.55e+00 bond pdb=" CB PRO a 579 " pdb=" CG PRO a 579 " ideal model delta sigma weight residual 1.492 1.552 -0.060 5.00e-02 4.00e+02 1.44e+00 bond pdb=" CG GLU d 536 " pdb=" CD GLU d 536 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.43e+00 bond pdb=" CG GLU k 536 " pdb=" CD GLU k 536 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.42e+00 ... (remaining 50707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 66219 1.74 - 3.48: 1788 3.48 - 5.22: 365 5.22 - 6.95: 72 6.95 - 8.69: 4 Bond angle restraints: 68448 Sorted by residual: angle pdb=" N GLU d 536 " pdb=" CA GLU d 536 " pdb=" CB GLU d 536 " ideal model delta sigma weight residual 110.28 116.64 -6.36 1.55e+00 4.16e-01 1.68e+01 angle pdb=" N GLU f 536 " pdb=" CA GLU f 536 " pdb=" CB GLU f 536 " ideal model delta sigma weight residual 110.28 116.64 -6.36 1.55e+00 4.16e-01 1.68e+01 angle pdb=" N GLU i 536 " pdb=" CA GLU i 536 " pdb=" CB GLU i 536 " ideal model delta sigma weight residual 110.28 116.55 -6.27 1.55e+00 4.16e-01 1.63e+01 angle pdb=" N GLU h 536 " pdb=" CA GLU h 536 " pdb=" CB GLU h 536 " ideal model delta sigma weight residual 110.28 116.49 -6.21 1.55e+00 4.16e-01 1.60e+01 angle pdb=" N GLU k 536 " pdb=" CA GLU k 536 " pdb=" CB GLU k 536 " ideal model delta sigma weight residual 110.28 116.40 -6.12 1.55e+00 4.16e-01 1.56e+01 ... (remaining 68443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 26959 17.09 - 34.19: 3269 34.19 - 51.28: 548 51.28 - 68.38: 81 68.38 - 85.47: 79 Dihedral angle restraints: 30936 sinusoidal: 12972 harmonic: 17964 Sorted by residual: dihedral pdb=" CA SER l 448 " pdb=" C SER l 448 " pdb=" N VAL l 449 " pdb=" CA VAL l 449 " ideal model delta harmonic sigma weight residual -180.00 -124.63 -55.37 0 5.00e+00 4.00e-02 1.23e+02 dihedral pdb=" CA VAL g 515 " pdb=" C VAL g 515 " pdb=" N THR g 516 " pdb=" CA THR g 516 " ideal model delta harmonic sigma weight residual 180.00 -147.29 -32.71 0 5.00e+00 4.00e-02 4.28e+01 dihedral pdb=" CA VAL d 515 " pdb=" C VAL d 515 " pdb=" N THR d 516 " pdb=" CA THR d 516 " ideal model delta harmonic sigma weight residual -180.00 -147.32 -32.68 0 5.00e+00 4.00e-02 4.27e+01 ... (remaining 30933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 6171 0.055 - 0.110: 1169 0.110 - 0.165: 150 0.165 - 0.220: 17 0.220 - 0.275: 5 Chirality restraints: 7512 Sorted by residual: chirality pdb=" CB ILE b 484 " pdb=" CA ILE b 484 " pdb=" CG1 ILE b 484 " pdb=" CG2 ILE b 484 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CB ILE e 484 " pdb=" CA ILE e 484 " pdb=" CG1 ILE e 484 " pdb=" CG2 ILE e 484 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CB ILE j 484 " pdb=" CA ILE j 484 " pdb=" CG1 ILE j 484 " pdb=" CG2 ILE j 484 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 7509 not shown) Planarity restraints: 8976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN h 503 " 0.053 5.00e-02 4.00e+02 8.04e-02 1.03e+01 pdb=" N PRO h 504 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO h 504 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO h 504 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN f 503 " -0.050 5.00e-02 4.00e+02 7.61e-02 9.26e+00 pdb=" N PRO f 504 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO f 504 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO f 504 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN k 503 " 0.049 5.00e-02 4.00e+02 7.38e-02 8.73e+00 pdb=" N PRO k 504 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO k 504 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO k 504 " 0.041 5.00e-02 4.00e+02 ... (remaining 8973 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 1062 2.65 - 3.21: 49433 3.21 - 3.77: 79885 3.77 - 4.34: 104348 4.34 - 4.90: 168182 Nonbonded interactions: 402910 Sorted by model distance: nonbonded pdb=" OD2 ASP j 573 " pdb=" NH1 ARG j 574 " model vdw 2.087 3.120 nonbonded pdb=" OD2 ASP h 573 " pdb=" NH1 ARG h 574 " model vdw 2.090 3.120 nonbonded pdb=" NE2 GLN f 126 " pdb=" O ARG g 330 " model vdw 2.191 3.120 nonbonded pdb=" NE2 GLN e 126 " pdb=" O ARG l 330 " model vdw 2.197 3.120 nonbonded pdb=" O LEU g 478 " pdb=" ND1 HIS g 482 " model vdw 2.211 3.120 ... (remaining 402905 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } 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 group one per residue 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: 1.010 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: 0.040 Extract box with map and model: 1.790 Check model and map are aligned: 0.320 Set scattering table: 0.430 Process input model: 78.340 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 50712 Z= 0.175 Angle : 0.690 8.693 68448 Z= 0.376 Chirality : 0.044 0.275 7512 Planarity : 0.005 0.100 8976 Dihedral : 14.932 85.470 19320 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.75 % Allowed : 16.52 % Favored : 82.73 % Rotamer: Outliers : 0.11 % Allowed : 0.55 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.66 (0.11), residues: 6108 helix: 0.25 (0.10), residues: 2604 sheet: -0.53 (0.29), residues: 468 loop : -4.05 (0.09), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP c 576 HIS 0.010 0.001 HIS j 482 PHE 0.017 0.001 PHE i 467 TYR 0.010 0.001 TYR g 412 ARG 0.006 0.000 ARG h 465 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12216 Ramachandran restraints generated. 6108 Oldfield, 0 Emsley, 6108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12216 Ramachandran restraints generated. 6108 Oldfield, 0 Emsley, 6108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 333 time to evaluate : 4.300 Fit side-chains REVERT: a 524 LYS cc_start: 0.9073 (mptt) cc_final: 0.8481 (tptt) REVERT: c 524 LYS cc_start: 0.8952 (mptt) cc_final: 0.8612 (tptt) REVERT: f 130 MET cc_start: 0.9123 (mmm) cc_final: 0.8760 (mmt) REVERT: f 528 MET cc_start: 0.9459 (tmm) cc_final: 0.9257 (tmm) REVERT: h 131 MET cc_start: 0.8866 (mmm) cc_final: 0.8465 (mmt) REVERT: h 524 LYS cc_start: 0.8920 (mptt) cc_final: 0.8510 (tptt) REVERT: i 447 MET cc_start: 0.8150 (ttt) cc_final: 0.7919 (tpt) REVERT: i 528 MET cc_start: 0.9325 (tmm) cc_final: 0.8988 (tmm) REVERT: j 130 MET cc_start: 0.9117 (mmm) cc_final: 0.8627 (mmt) REVERT: j 528 MET cc_start: 0.9213 (tmm) cc_final: 0.8811 (tmm) REVERT: k 417 ARG cc_start: 0.8929 (ptp-110) cc_final: 0.8445 (ptm160) REVERT: k 528 MET cc_start: 0.9191 (tmm) cc_final: 0.8932 (tmm) REVERT: l 414 MET cc_start: 0.8913 (tpp) cc_final: 0.8436 (tpp) outliers start: 6 outliers final: 0 residues processed: 339 average time/residue: 0.4876 time to fit residues: 279.7385 Evaluate side-chains 298 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 4.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 516 optimal weight: 1.9990 chunk 463 optimal weight: 6.9990 chunk 257 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 312 optimal weight: 10.0000 chunk 247 optimal weight: 0.1980 chunk 479 optimal weight: 40.0000 chunk 185 optimal weight: 20.0000 chunk 291 optimal weight: 30.0000 chunk 357 optimal weight: 60.0000 chunk 555 optimal weight: 6.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 530 HIS ** a 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 530 HIS ** c 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 450 ASN ** f 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 558 ASN ** h 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 367 GLN l 527 GLN ** l 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 50712 Z= 0.192 Angle : 0.672 6.729 68448 Z= 0.353 Chirality : 0.043 0.187 7512 Planarity : 0.004 0.067 8976 Dihedral : 5.332 54.931 6768 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.75 % Allowed : 16.26 % Favored : 82.99 % Rotamer: Outliers : 0.59 % Allowed : 7.97 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.60 (0.11), residues: 6108 helix: 0.37 (0.10), residues: 2652 sheet: -0.53 (0.29), residues: 468 loop : -4.17 (0.09), residues: 2988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP g 124 HIS 0.010 0.001 HIS d 530 PHE 0.013 0.001 PHE l 476 TYR 0.011 0.001 TYR l 329 ARG 0.009 0.000 ARG d 474 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12216 Ramachandran restraints generated. 6108 Oldfield, 0 Emsley, 6108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12216 Ramachandran restraints generated. 6108 Oldfield, 0 Emsley, 6108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 300 time to evaluate : 4.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 524 LYS cc_start: 0.9122 (mptt) cc_final: 0.8553 (tptt) REVERT: b 396 MET cc_start: 0.7728 (tmm) cc_final: 0.7515 (tmm) REVERT: b 524 LYS cc_start: 0.8985 (mmtt) cc_final: 0.8625 (mmtt) REVERT: c 396 MET cc_start: 0.7490 (tmm) cc_final: 0.7253 (tmm) REVERT: c 524 LYS cc_start: 0.9143 (mptt) cc_final: 0.8642 (tptt) REVERT: e 524 LYS cc_start: 0.9156 (mmtt) cc_final: 0.8565 (tptt) REVERT: f 359 MET cc_start: 0.8597 (ppp) cc_final: 0.8396 (ppp) REVERT: f 524 LYS cc_start: 0.9223 (mmtt) cc_final: 0.8671 (tptt) REVERT: g 453 MET cc_start: 0.8456 (mpp) cc_final: 0.7898 (ptt) REVERT: g 524 LYS cc_start: 0.9167 (mmtt) cc_final: 0.8826 (mmtt) REVERT: h 537 MET cc_start: 0.8831 (mmm) cc_final: 0.8230 (mmm) REVERT: i 474 ARG cc_start: 0.8859 (ttp80) cc_final: 0.8633 (ttp80) REVERT: i 528 MET cc_start: 0.9327 (tmm) cc_final: 0.8986 (tmm) REVERT: j 528 MET cc_start: 0.9299 (tmm) cc_final: 0.9048 (tmm) REVERT: k 524 LYS cc_start: 0.9234 (mmtt) cc_final: 0.8689 (tptt) REVERT: l 367 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7381 (tm-30) REVERT: l 524 LYS cc_start: 0.9011 (mmtt) cc_final: 0.8455 (ttmt) outliers start: 32 outliers final: 17 residues processed: 322 average time/residue: 0.4816 time to fit residues: 266.1193 Evaluate side-chains 310 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 292 time to evaluate : 4.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 377 VAL Chi-restraints excluded: chain a residue 536 GLU Chi-restraints excluded: chain b residue 338 MET Chi-restraints excluded: chain b residue 536 GLU Chi-restraints excluded: chain c residue 536 GLU Chi-restraints excluded: chain d residue 377 VAL Chi-restraints excluded: chain e residue 362 ILE Chi-restraints excluded: chain e residue 377 VAL Chi-restraints excluded: chain f residue 377 VAL Chi-restraints excluded: chain f residue 536 GLU Chi-restraints excluded: chain g residue 377 VAL Chi-restraints excluded: chain i residue 377 VAL Chi-restraints excluded: chain i residue 530 HIS Chi-restraints excluded: chain i residue 536 GLU Chi-restraints excluded: chain j residue 377 VAL Chi-restraints excluded: chain l residue 367 GLN Chi-restraints excluded: chain l residue 482 HIS Chi-restraints excluded: chain l residue 536 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 308 optimal weight: 9.9990 chunk 172 optimal weight: 20.0000 chunk 462 optimal weight: 9.9990 chunk 378 optimal weight: 20.0000 chunk 153 optimal weight: 60.0000 chunk 556 optimal weight: 1.9990 chunk 601 optimal weight: 50.0000 chunk 495 optimal weight: 20.0000 chunk 552 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 446 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 37 GLN ** a 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 37 GLN ** b 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 37 GLN c 367 GLN c 450 ASN ** c 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 37 GLN ** e 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 37 GLN ** f 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 37 GLN g 367 GLN g 450 ASN ** g 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 37 GLN ** j 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 37 GLN l 367 GLN ** l 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 558 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 50712 Z= 0.218 Angle : 0.674 9.417 68448 Z= 0.354 Chirality : 0.043 0.178 7512 Planarity : 0.004 0.060 8976 Dihedral : 5.312 53.791 6768 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.75 % Allowed : 16.18 % Favored : 83.07 % Rotamer: Outliers : 1.04 % Allowed : 12.60 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.54 (0.11), residues: 6108 helix: 0.45 (0.10), residues: 2652 sheet: -0.52 (0.29), residues: 468 loop : -4.15 (0.09), residues: 2988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP c 576 HIS 0.010 0.001 HIS d 530 PHE 0.010 0.001 PHE l 476 TYR 0.013 0.001 TYR l 329 ARG 0.016 0.000 ARG f 474 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12216 Ramachandran restraints generated. 6108 Oldfield, 0 Emsley, 6108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12216 Ramachandran restraints generated. 6108 Oldfield, 0 Emsley, 6108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 301 time to evaluate : 4.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 524 LYS cc_start: 0.9148 (mptt) cc_final: 0.8626 (tptt) REVERT: c 367 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: c 396 MET cc_start: 0.7598 (tmm) cc_final: 0.7241 (tmm) REVERT: c 524 LYS cc_start: 0.9181 (mptt) cc_final: 0.8710 (tptt) REVERT: e 447 MET cc_start: 0.8326 (tpt) cc_final: 0.7830 (tpp) REVERT: e 524 LYS cc_start: 0.9169 (mmtt) cc_final: 0.8603 (tptt) REVERT: f 130 MET cc_start: 0.9243 (mmt) cc_final: 0.9014 (mmt) REVERT: f 524 LYS cc_start: 0.9236 (mmtt) cc_final: 0.8739 (tptt) REVERT: f 528 MET cc_start: 0.9423 (tmm) cc_final: 0.9183 (tmm) REVERT: g 367 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7399 (tm-30) REVERT: g 449 VAL cc_start: 0.9354 (OUTLIER) cc_final: 0.8695 (m) REVERT: g 453 MET cc_start: 0.8302 (mpp) cc_final: 0.7772 (ptt) REVERT: g 524 LYS cc_start: 0.9218 (mmtt) cc_final: 0.9001 (mmtt) REVERT: h 73 MET cc_start: 0.8976 (mmt) cc_final: 0.8698 (mmt) REVERT: h 466 MET cc_start: 0.8797 (mmm) cc_final: 0.8573 (mmm) REVERT: h 524 LYS cc_start: 0.9262 (mmtt) cc_final: 0.8770 (tptt) REVERT: i 396 MET cc_start: 0.7609 (tmm) cc_final: 0.7241 (tmm) REVERT: j 130 MET cc_start: 0.9212 (mmm) cc_final: 0.8770 (mmt) REVERT: j 528 MET cc_start: 0.9341 (tmm) cc_final: 0.9040 (tmm) REVERT: j 573 ASP cc_start: 0.7194 (OUTLIER) cc_final: 0.6951 (t0) REVERT: k 131 MET cc_start: 0.9019 (mmt) cc_final: 0.8671 (mmt) REVERT: k 417 ARG cc_start: 0.8903 (ptp-110) cc_final: 0.8269 (ptm-80) REVERT: k 524 LYS cc_start: 0.9290 (mmtt) cc_final: 0.8796 (tptt) REVERT: l 130 MET cc_start: 0.9062 (mmm) cc_final: 0.8560 (mmm) REVERT: l 367 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7559 (tm-30) REVERT: l 524 LYS cc_start: 0.9193 (mmtt) cc_final: 0.8590 (tttm) outliers start: 57 outliers final: 24 residues processed: 345 average time/residue: 0.4930 time to fit residues: 294.1981 Evaluate side-chains 325 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 296 time to evaluate : 4.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 377 VAL Chi-restraints excluded: chain a residue 536 GLU Chi-restraints excluded: chain b residue 377 VAL Chi-restraints excluded: chain b residue 536 GLU Chi-restraints excluded: chain c residue 367 GLN Chi-restraints excluded: chain c residue 377 VAL Chi-restraints excluded: chain c residue 536 GLU Chi-restraints excluded: chain d residue 377 VAL Chi-restraints excluded: chain e residue 377 VAL Chi-restraints excluded: chain f residue 377 VAL Chi-restraints excluded: chain f residue 536 GLU Chi-restraints excluded: chain g residue 367 GLN Chi-restraints excluded: chain g residue 377 VAL Chi-restraints excluded: chain g residue 449 VAL Chi-restraints excluded: chain g residue 573 ASP Chi-restraints excluded: chain h residue 377 VAL Chi-restraints excluded: chain h residue 482 HIS Chi-restraints excluded: chain i residue 377 VAL Chi-restraints excluded: chain i residue 530 HIS Chi-restraints excluded: chain i residue 536 GLU Chi-restraints excluded: chain j residue 377 VAL Chi-restraints excluded: chain j residue 573 ASP Chi-restraints excluded: chain k residue 377 VAL Chi-restraints excluded: chain k residue 482 HIS Chi-restraints excluded: chain k residue 536 GLU Chi-restraints excluded: chain l residue 367 GLN Chi-restraints excluded: chain l residue 377 VAL Chi-restraints excluded: chain l residue 482 HIS Chi-restraints excluded: chain l residue 536 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 550 optimal weight: 0.7980 chunk 418 optimal weight: 7.9990 chunk 288 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 chunk 265 optimal weight: 8.9990 chunk 373 optimal weight: 50.0000 chunk 558 optimal weight: 10.0000 chunk 591 optimal weight: 4.9990 chunk 291 optimal weight: 9.9990 chunk 529 optimal weight: 0.0050 chunk 159 optimal weight: 8.9990 overall best weight: 4.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 367 GLN ** a 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 527 GLN ** b 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 367 GLN ** f 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 367 GLN k 554 GLN l 385 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 50712 Z= 0.190 Angle : 0.674 8.159 68448 Z= 0.351 Chirality : 0.042 0.174 7512 Planarity : 0.004 0.058 8976 Dihedral : 5.245 53.666 6768 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.75 % Allowed : 16.08 % Favored : 83.17 % Rotamer: Outliers : 1.68 % Allowed : 14.80 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.49 (0.11), residues: 6108 helix: 0.49 (0.10), residues: 2652 sheet: -0.46 (0.29), residues: 468 loop : -4.13 (0.09), residues: 2988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP k 576 HIS 0.010 0.001 HIS h 482 PHE 0.009 0.001 PHE e 467 TYR 0.011 0.001 TYR k 329 ARG 0.007 0.000 ARG f 474 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12216 Ramachandran restraints generated. 6108 Oldfield, 0 Emsley, 6108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12216 Ramachandran restraints generated. 6108 Oldfield, 0 Emsley, 6108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 304 time to evaluate : 4.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 367 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7320 (tm-30) REVERT: a 524 LYS cc_start: 0.9149 (mptt) cc_final: 0.8654 (tttt) REVERT: b 524 LYS cc_start: 0.9079 (mmtt) cc_final: 0.8267 (tptm) REVERT: c 396 MET cc_start: 0.7634 (tmm) cc_final: 0.7287 (tmm) REVERT: c 524 LYS cc_start: 0.9199 (mptt) cc_final: 0.8767 (tptt) REVERT: e 359 MET cc_start: 0.8579 (ppp) cc_final: 0.8365 (ppp) REVERT: e 447 MET cc_start: 0.8284 (tpt) cc_final: 0.8079 (tpt) REVERT: e 524 LYS cc_start: 0.9136 (mmtt) cc_final: 0.8570 (tptt) REVERT: f 359 MET cc_start: 0.8710 (ppp) cc_final: 0.8508 (ppp) REVERT: f 367 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7382 (tm-30) REVERT: f 447 MET cc_start: 0.8442 (tpt) cc_final: 0.7947 (tpt) REVERT: f 524 LYS cc_start: 0.9218 (mmtt) cc_final: 0.8657 (tptt) REVERT: h 73 MET cc_start: 0.9005 (mmt) cc_final: 0.8743 (mmt) REVERT: h 524 LYS cc_start: 0.9234 (mmtt) cc_final: 0.8716 (tptt) REVERT: i 528 MET cc_start: 0.9362 (tmm) cc_final: 0.9127 (tmm) REVERT: j 130 MET cc_start: 0.9196 (mmm) cc_final: 0.8751 (mmt) REVERT: j 430 ASP cc_start: 0.8245 (m-30) cc_final: 0.7966 (p0) REVERT: j 528 MET cc_start: 0.9351 (tmm) cc_final: 0.9083 (tmm) REVERT: k 131 MET cc_start: 0.8976 (mmt) cc_final: 0.8564 (mmt) REVERT: k 367 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7539 (tm-30) REVERT: k 417 ARG cc_start: 0.8890 (ptp-110) cc_final: 0.8431 (ptm160) REVERT: k 524 LYS cc_start: 0.9267 (mmtt) cc_final: 0.8771 (tptt) REVERT: l 524 LYS cc_start: 0.9175 (mmtt) cc_final: 0.8542 (tttm) REVERT: l 537 MET cc_start: 0.8751 (mmm) cc_final: 0.8473 (mmm) outliers start: 92 outliers final: 24 residues processed: 384 average time/residue: 0.4559 time to fit residues: 303.6225 Evaluate side-chains 325 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 298 time to evaluate : 4.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 367 GLN Chi-restraints excluded: chain a residue 377 VAL Chi-restraints excluded: chain a residue 482 HIS Chi-restraints excluded: chain a residue 536 GLU Chi-restraints excluded: chain b residue 377 VAL Chi-restraints excluded: chain b residue 536 GLU Chi-restraints excluded: chain c residue 377 VAL Chi-restraints excluded: chain c residue 482 HIS Chi-restraints excluded: chain c residue 536 GLU Chi-restraints excluded: chain d residue 377 VAL Chi-restraints excluded: chain e residue 377 VAL Chi-restraints excluded: chain f residue 367 GLN Chi-restraints excluded: chain f residue 377 VAL Chi-restraints excluded: chain f residue 536 GLU Chi-restraints excluded: chain f residue 569 TYR Chi-restraints excluded: chain h residue 377 VAL Chi-restraints excluded: chain h residue 569 TYR Chi-restraints excluded: chain i residue 377 VAL Chi-restraints excluded: chain i residue 536 GLU Chi-restraints excluded: chain j residue 377 VAL Chi-restraints excluded: chain k residue 367 GLN Chi-restraints excluded: chain k residue 482 HIS Chi-restraints excluded: chain k residue 536 GLU Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain l residue 377 VAL Chi-restraints excluded: chain l residue 482 HIS Chi-restraints excluded: chain l residue 562 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 492 optimal weight: 7.9990 chunk 335 optimal weight: 30.0000 chunk 8 optimal weight: 20.0000 chunk 440 optimal weight: 8.9990 chunk 244 optimal weight: 9.9990 chunk 504 optimal weight: 1.9990 chunk 408 optimal weight: 60.0000 chunk 0 optimal weight: 70.0000 chunk 302 optimal weight: 8.9990 chunk 530 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 37 GLN ** h 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 50712 Z= 0.231 Angle : 0.694 9.388 68448 Z= 0.362 Chirality : 0.043 0.175 7512 Planarity : 0.004 0.070 8976 Dihedral : 5.278 54.252 6768 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.75 % Allowed : 16.39 % Favored : 82.86 % Rotamer: Outliers : 1.79 % Allowed : 16.30 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.45 (0.11), residues: 6108 helix: 0.52 (0.10), residues: 2652 sheet: -0.46 (0.29), residues: 468 loop : -4.11 (0.09), residues: 2988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP c 576 HIS 0.011 0.001 HIS d 530 PHE 0.010 0.001 PHE d 111 TYR 0.013 0.001 TYR l 329 ARG 0.014 0.000 ARG i 474 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12216 Ramachandran restraints generated. 6108 Oldfield, 0 Emsley, 6108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12216 Ramachandran restraints generated. 6108 Oldfield, 0 Emsley, 6108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 299 time to evaluate : 4.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 396 MET cc_start: 0.7971 (tmm) cc_final: 0.7732 (tmm) REVERT: a 524 LYS cc_start: 0.9191 (mptt) cc_final: 0.8718 (tttt) REVERT: c 524 LYS cc_start: 0.9207 (mptt) cc_final: 0.8793 (tptt) REVERT: d 130 MET cc_start: 0.9214 (mmt) cc_final: 0.8856 (mmt) REVERT: d 524 LYS cc_start: 0.9217 (mmtt) cc_final: 0.8255 (tptt) REVERT: e 359 MET cc_start: 0.8610 (ppp) cc_final: 0.8405 (ppp) REVERT: f 417 ARG cc_start: 0.8958 (ptp-110) cc_final: 0.8501 (ptm160) REVERT: f 447 MET cc_start: 0.8504 (tpt) cc_final: 0.8036 (tpt) REVERT: f 524 LYS cc_start: 0.9215 (mmtt) cc_final: 0.8678 (tptt) REVERT: f 528 MET cc_start: 0.9433 (tmm) cc_final: 0.9146 (tmm) REVERT: g 449 VAL cc_start: 0.9355 (OUTLIER) cc_final: 0.8764 (m) REVERT: g 453 MET cc_start: 0.8441 (mpp) cc_final: 0.7906 (ptt) REVERT: g 524 LYS cc_start: 0.9117 (mmtt) cc_final: 0.8846 (mmtt) REVERT: h 131 MET cc_start: 0.9113 (mmt) cc_final: 0.8711 (mmt) REVERT: h 396 MET cc_start: 0.8104 (tmm) cc_final: 0.7809 (tmm) REVERT: h 524 LYS cc_start: 0.9255 (mmtt) cc_final: 0.8806 (tptt) REVERT: i 528 MET cc_start: 0.9366 (tmm) cc_final: 0.8996 (tmm) REVERT: j 430 ASP cc_start: 0.8285 (m-30) cc_final: 0.7982 (p0) REVERT: j 528 MET cc_start: 0.9380 (tmm) cc_final: 0.9107 (tmm) REVERT: j 573 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.6941 (t0) REVERT: k 367 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7520 (tm-30) REVERT: k 447 MET cc_start: 0.8510 (tmm) cc_final: 0.8084 (tmm) REVERT: k 524 LYS cc_start: 0.9260 (mmtt) cc_final: 0.8783 (tptt) REVERT: k 537 MET cc_start: 0.8929 (mmm) cc_final: 0.8685 (mmm) REVERT: l 524 LYS cc_start: 0.9197 (mmtt) cc_final: 0.8581 (tttm) outliers start: 98 outliers final: 41 residues processed: 382 average time/residue: 0.4665 time to fit residues: 306.1656 Evaluate side-chains 339 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 295 time to evaluate : 4.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 377 VAL Chi-restraints excluded: chain a residue 482 HIS Chi-restraints excluded: chain a residue 536 GLU Chi-restraints excluded: chain a residue 569 TYR Chi-restraints excluded: chain b residue 377 VAL Chi-restraints excluded: chain b residue 536 GLU Chi-restraints excluded: chain b residue 549 VAL Chi-restraints excluded: chain c residue 377 VAL Chi-restraints excluded: chain c residue 482 HIS Chi-restraints excluded: chain c residue 536 GLU Chi-restraints excluded: chain c residue 569 TYR Chi-restraints excluded: chain d residue 377 VAL Chi-restraints excluded: chain d residue 482 HIS Chi-restraints excluded: chain e residue 362 ILE Chi-restraints excluded: chain e residue 377 VAL Chi-restraints excluded: chain e residue 482 HIS Chi-restraints excluded: chain f residue 377 VAL Chi-restraints excluded: chain f residue 482 HIS Chi-restraints excluded: chain f residue 495 LEU Chi-restraints excluded: chain f residue 530 HIS Chi-restraints excluded: chain f residue 536 GLU Chi-restraints excluded: chain f residue 569 TYR Chi-restraints excluded: chain g residue 377 VAL Chi-restraints excluded: chain g residue 449 VAL Chi-restraints excluded: chain g residue 482 HIS Chi-restraints excluded: chain h residue 377 VAL Chi-restraints excluded: chain h residue 569 TYR Chi-restraints excluded: chain i residue 377 VAL Chi-restraints excluded: chain i residue 482 HIS Chi-restraints excluded: chain i residue 530 HIS Chi-restraints excluded: chain i residue 536 GLU Chi-restraints excluded: chain i residue 569 TYR Chi-restraints excluded: chain i residue 573 ASP Chi-restraints excluded: chain j residue 377 VAL Chi-restraints excluded: chain j residue 549 VAL Chi-restraints excluded: chain j residue 573 ASP Chi-restraints excluded: chain k residue 367 GLN Chi-restraints excluded: chain k residue 377 VAL Chi-restraints excluded: chain k residue 482 HIS Chi-restraints excluded: chain k residue 569 TYR Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain l residue 377 VAL Chi-restraints excluded: chain l residue 482 HIS Chi-restraints excluded: chain l residue 562 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 199 optimal weight: 6.9990 chunk 532 optimal weight: 50.0000 chunk 116 optimal weight: 6.9990 chunk 347 optimal weight: 0.0570 chunk 146 optimal weight: 7.9990 chunk 592 optimal weight: 40.0000 chunk 491 optimal weight: 7.9990 chunk 274 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 195 optimal weight: 30.0000 chunk 310 optimal weight: 6.9990 overall best weight: 4.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 367 GLN ** d 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 367 GLN ** j 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 50712 Z= 0.197 Angle : 0.694 10.882 68448 Z= 0.360 Chirality : 0.043 0.173 7512 Planarity : 0.004 0.058 8976 Dihedral : 5.233 53.710 6768 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.75 % Allowed : 16.32 % Favored : 82.92 % Rotamer: Outliers : 1.58 % Allowed : 17.86 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.42 (0.11), residues: 6108 helix: 0.54 (0.10), residues: 2652 sheet: -0.42 (0.29), residues: 468 loop : -4.07 (0.10), residues: 2988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP e 576 HIS 0.010 0.001 HIS i 530 PHE 0.011 0.001 PHE d 111 TYR 0.011 0.001 TYR l 329 ARG 0.007 0.000 ARG b 574 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12216 Ramachandran restraints generated. 6108 Oldfield, 0 Emsley, 6108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12216 Ramachandran restraints generated. 6108 Oldfield, 0 Emsley, 6108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 307 time to evaluate : 4.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 524 LYS cc_start: 0.9215 (mptt) cc_final: 0.8753 (tptt) REVERT: b 524 LYS cc_start: 0.9182 (mmtt) cc_final: 0.8431 (tptm) REVERT: c 131 MET cc_start: 0.9029 (mmt) cc_final: 0.8660 (mmt) REVERT: c 524 LYS cc_start: 0.9223 (mptt) cc_final: 0.8698 (tptm) REVERT: d 130 MET cc_start: 0.9209 (mmt) cc_final: 0.8870 (mmt) REVERT: d 367 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: d 396 MET cc_start: 0.7989 (tmm) cc_final: 0.7783 (tmm) REVERT: d 524 LYS cc_start: 0.9130 (mmtt) cc_final: 0.8230 (tptt) REVERT: e 359 MET cc_start: 0.8631 (ppp) cc_final: 0.8413 (ppp) REVERT: e 396 MET cc_start: 0.7791 (tmm) cc_final: 0.7583 (tmm) REVERT: e 447 MET cc_start: 0.8325 (tpt) cc_final: 0.7905 (tpt) REVERT: e 524 LYS cc_start: 0.9198 (mmtt) cc_final: 0.8634 (tptt) REVERT: f 73 MET cc_start: 0.8765 (mmt) cc_final: 0.8435 (mmt) REVERT: f 417 ARG cc_start: 0.8963 (ptp-110) cc_final: 0.8621 (ptm160) REVERT: f 447 MET cc_start: 0.8414 (tpt) cc_final: 0.8030 (tpt) REVERT: f 524 LYS cc_start: 0.9169 (mmtt) cc_final: 0.8634 (tptt) REVERT: f 528 MET cc_start: 0.9403 (tmm) cc_final: 0.9142 (tmm) REVERT: f 562 GLU cc_start: 0.8321 (tp30) cc_final: 0.8068 (tm-30) REVERT: g 449 VAL cc_start: 0.9342 (OUTLIER) cc_final: 0.8765 (m) REVERT: g 453 MET cc_start: 0.8336 (mpp) cc_final: 0.7824 (ptt) REVERT: g 524 LYS cc_start: 0.9088 (mmtt) cc_final: 0.8825 (mmtt) REVERT: h 73 MET cc_start: 0.8915 (mmt) cc_final: 0.8661 (mmt) REVERT: h 524 LYS cc_start: 0.9222 (mmtt) cc_final: 0.8711 (tptt) REVERT: i 396 MET cc_start: 0.7731 (tmm) cc_final: 0.7290 (tmm) REVERT: i 528 MET cc_start: 0.9360 (tmm) cc_final: 0.9081 (tmm) REVERT: j 367 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7405 (tm-30) REVERT: j 430 ASP cc_start: 0.8269 (m-30) cc_final: 0.7982 (p0) REVERT: j 528 MET cc_start: 0.9370 (tmm) cc_final: 0.9137 (tmm) REVERT: j 573 ASP cc_start: 0.7265 (OUTLIER) cc_final: 0.6830 (t0) REVERT: k 447 MET cc_start: 0.8498 (tmm) cc_final: 0.8219 (tmm) REVERT: k 524 LYS cc_start: 0.9219 (mmtt) cc_final: 0.8761 (tptt) REVERT: l 559 ILE cc_start: 0.9712 (OUTLIER) cc_final: 0.9511 (mm) outliers start: 86 outliers final: 50 residues processed: 377 average time/residue: 0.4612 time to fit residues: 300.0198 Evaluate side-chains 352 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 297 time to evaluate : 4.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 110 LEU Chi-restraints excluded: chain a residue 377 VAL Chi-restraints excluded: chain a residue 482 HIS Chi-restraints excluded: chain a residue 536 GLU Chi-restraints excluded: chain a residue 569 TYR Chi-restraints excluded: chain b residue 377 VAL Chi-restraints excluded: chain b residue 536 GLU Chi-restraints excluded: chain b residue 549 VAL Chi-restraints excluded: chain b residue 569 TYR Chi-restraints excluded: chain c residue 377 VAL Chi-restraints excluded: chain c residue 482 HIS Chi-restraints excluded: chain c residue 536 GLU Chi-restraints excluded: chain c residue 569 TYR Chi-restraints excluded: chain d residue 110 LEU Chi-restraints excluded: chain d residue 367 GLN Chi-restraints excluded: chain d residue 377 VAL Chi-restraints excluded: chain d residue 482 HIS Chi-restraints excluded: chain d residue 569 TYR Chi-restraints excluded: chain e residue 130 MET Chi-restraints excluded: chain e residue 377 VAL Chi-restraints excluded: chain e residue 482 HIS Chi-restraints excluded: chain e residue 569 TYR Chi-restraints excluded: chain f residue 110 LEU Chi-restraints excluded: chain f residue 377 VAL Chi-restraints excluded: chain f residue 482 HIS Chi-restraints excluded: chain f residue 536 GLU Chi-restraints excluded: chain f residue 549 VAL Chi-restraints excluded: chain f residue 569 TYR Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain g residue 377 VAL Chi-restraints excluded: chain g residue 449 VAL Chi-restraints excluded: chain g residue 482 HIS Chi-restraints excluded: chain g residue 569 TYR Chi-restraints excluded: chain h residue 110 LEU Chi-restraints excluded: chain h residue 377 VAL Chi-restraints excluded: chain h residue 482 HIS Chi-restraints excluded: chain h residue 569 TYR Chi-restraints excluded: chain i residue 377 VAL Chi-restraints excluded: chain i residue 482 HIS Chi-restraints excluded: chain i residue 536 GLU Chi-restraints excluded: chain i residue 569 TYR Chi-restraints excluded: chain i residue 573 ASP Chi-restraints excluded: chain j residue 367 GLN Chi-restraints excluded: chain j residue 377 VAL Chi-restraints excluded: chain j residue 549 VAL Chi-restraints excluded: chain j residue 569 TYR Chi-restraints excluded: chain j residue 573 ASP Chi-restraints excluded: chain k residue 377 VAL Chi-restraints excluded: chain k residue 482 HIS Chi-restraints excluded: chain k residue 569 TYR Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain l residue 377 VAL Chi-restraints excluded: chain l residue 482 HIS Chi-restraints excluded: chain l residue 559 ILE Chi-restraints excluded: chain l residue 569 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 570 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 337 optimal weight: 10.0000 chunk 432 optimal weight: 20.0000 chunk 335 optimal weight: 20.0000 chunk 498 optimal weight: 6.9990 chunk 330 optimal weight: 20.0000 chunk 589 optimal weight: 8.9990 chunk 369 optimal weight: 20.0000 chunk 359 optimal weight: 20.0000 chunk 272 optimal weight: 30.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 480 HIS ** b 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 480 HIS ** e 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 480 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 50712 Z= 0.260 Angle : 0.727 12.303 68448 Z= 0.378 Chirality : 0.044 0.234 7512 Planarity : 0.004 0.060 8976 Dihedral : 5.332 53.759 6768 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.77 % Allowed : 16.55 % Favored : 82.68 % Rotamer: Outliers : 1.36 % Allowed : 19.18 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.45 (0.11), residues: 6108 helix: 0.51 (0.10), residues: 2652 sheet: -0.48 (0.29), residues: 468 loop : -4.09 (0.09), residues: 2988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP a 576 HIS 0.015 0.001 HIS k 530 PHE 0.014 0.001 PHE d 111 TYR 0.015 0.001 TYR f 329 ARG 0.010 0.000 ARG d 474 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12216 Ramachandran restraints generated. 6108 Oldfield, 0 Emsley, 6108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12216 Ramachandran restraints generated. 6108 Oldfield, 0 Emsley, 6108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 307 time to evaluate : 4.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 524 LYS cc_start: 0.9248 (mptt) cc_final: 0.8784 (tptt) REVERT: a 559 ILE cc_start: 0.9689 (OUTLIER) cc_final: 0.9398 (mm) REVERT: b 131 MET cc_start: 0.9022 (mmt) cc_final: 0.8627 (mmt) REVERT: b 524 LYS cc_start: 0.9225 (mmtt) cc_final: 0.8396 (tptm) REVERT: c 131 MET cc_start: 0.9115 (mmt) cc_final: 0.8759 (mmt) REVERT: c 524 LYS cc_start: 0.9270 (mptt) cc_final: 0.8813 (tptm) REVERT: d 524 LYS cc_start: 0.9181 (mmtt) cc_final: 0.8274 (tptm) REVERT: d 559 ILE cc_start: 0.9657 (OUTLIER) cc_final: 0.9434 (mm) REVERT: e 355 MET cc_start: 0.9301 (tpp) cc_final: 0.8963 (tpp) REVERT: e 359 MET cc_start: 0.8656 (ppp) cc_final: 0.8442 (ppp) REVERT: f 73 MET cc_start: 0.8811 (mmt) cc_final: 0.8493 (mmt) REVERT: f 131 MET cc_start: 0.8923 (mmt) cc_final: 0.8570 (mmt) REVERT: f 417 ARG cc_start: 0.8962 (ptp-110) cc_final: 0.8586 (ptm160) REVERT: g 359 MET cc_start: 0.8454 (ppp) cc_final: 0.8249 (ppp) REVERT: g 524 LYS cc_start: 0.9183 (mmtt) cc_final: 0.8912 (mmtt) REVERT: h 524 LYS cc_start: 0.9225 (mmtt) cc_final: 0.8766 (tptt) REVERT: i 528 MET cc_start: 0.9385 (tmm) cc_final: 0.9108 (tmm) REVERT: j 130 MET cc_start: 0.9221 (mmt) cc_final: 0.9004 (mmm) REVERT: j 355 MET cc_start: 0.9247 (tpp) cc_final: 0.8940 (tpp) REVERT: j 430 ASP cc_start: 0.8232 (m-30) cc_final: 0.8004 (p0) REVERT: j 528 MET cc_start: 0.9398 (tmm) cc_final: 0.9167 (tmm) REVERT: j 573 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.6852 (t0) REVERT: k 396 MET cc_start: 0.8246 (tmm) cc_final: 0.7841 (tmm) REVERT: l 524 LYS cc_start: 0.9295 (mmtt) cc_final: 0.8717 (tttm) REVERT: l 559 ILE cc_start: 0.9664 (OUTLIER) cc_final: 0.9399 (mm) outliers start: 74 outliers final: 52 residues processed: 362 average time/residue: 0.4646 time to fit residues: 289.0508 Evaluate side-chains 359 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 303 time to evaluate : 4.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 110 LEU Chi-restraints excluded: chain a residue 377 VAL Chi-restraints excluded: chain a residue 482 HIS Chi-restraints excluded: chain a residue 536 GLU Chi-restraints excluded: chain a residue 559 ILE Chi-restraints excluded: chain a residue 569 TYR Chi-restraints excluded: chain b residue 377 VAL Chi-restraints excluded: chain b residue 536 GLU Chi-restraints excluded: chain b residue 549 VAL Chi-restraints excluded: chain b residue 569 TYR Chi-restraints excluded: chain c residue 377 VAL Chi-restraints excluded: chain c residue 482 HIS Chi-restraints excluded: chain c residue 536 GLU Chi-restraints excluded: chain c residue 549 VAL Chi-restraints excluded: chain c residue 569 TYR Chi-restraints excluded: chain d residue 377 VAL Chi-restraints excluded: chain d residue 482 HIS Chi-restraints excluded: chain d residue 559 ILE Chi-restraints excluded: chain d residue 569 TYR Chi-restraints excluded: chain e residue 130 MET Chi-restraints excluded: chain e residue 362 ILE Chi-restraints excluded: chain e residue 377 VAL Chi-restraints excluded: chain e residue 482 HIS Chi-restraints excluded: chain e residue 569 TYR Chi-restraints excluded: chain f residue 110 LEU Chi-restraints excluded: chain f residue 362 ILE Chi-restraints excluded: chain f residue 377 VAL Chi-restraints excluded: chain f residue 482 HIS Chi-restraints excluded: chain f residue 536 GLU Chi-restraints excluded: chain f residue 549 VAL Chi-restraints excluded: chain f residue 569 TYR Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain g residue 377 VAL Chi-restraints excluded: chain g residue 482 HIS Chi-restraints excluded: chain g residue 569 TYR Chi-restraints excluded: chain h residue 377 VAL Chi-restraints excluded: chain h residue 482 HIS Chi-restraints excluded: chain h residue 569 TYR Chi-restraints excluded: chain i residue 377 VAL Chi-restraints excluded: chain i residue 482 HIS Chi-restraints excluded: chain i residue 536 GLU Chi-restraints excluded: chain i residue 569 TYR Chi-restraints excluded: chain j residue 377 VAL Chi-restraints excluded: chain j residue 549 VAL Chi-restraints excluded: chain j residue 569 TYR Chi-restraints excluded: chain j residue 573 ASP Chi-restraints excluded: chain k residue 377 VAL Chi-restraints excluded: chain k residue 482 HIS Chi-restraints excluded: chain k residue 549 VAL Chi-restraints excluded: chain k residue 569 TYR Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain l residue 377 VAL Chi-restraints excluded: chain l residue 482 HIS Chi-restraints excluded: chain l residue 549 VAL Chi-restraints excluded: chain l residue 559 ILE Chi-restraints excluded: chain l residue 569 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 364 optimal weight: 3.9990 chunk 235 optimal weight: 20.0000 chunk 352 optimal weight: 10.0000 chunk 177 optimal weight: 20.0000 chunk 115 optimal weight: 40.0000 chunk 114 optimal weight: 7.9990 chunk 375 optimal weight: 40.0000 chunk 401 optimal weight: 20.0000 chunk 291 optimal weight: 30.0000 chunk 54 optimal weight: 5.9990 chunk 463 optimal weight: 8.9990 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 50712 Z= 0.239 Angle : 0.727 12.741 68448 Z= 0.376 Chirality : 0.044 0.231 7512 Planarity : 0.004 0.060 8976 Dihedral : 5.363 54.164 6768 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.72 % Allowed : 16.73 % Favored : 82.55 % Rotamer: Outliers : 1.30 % Allowed : 19.71 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.46 (0.11), residues: 6108 helix: 0.49 (0.10), residues: 2652 sheet: -0.49 (0.29), residues: 468 loop : -4.08 (0.09), residues: 2988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP c 576 HIS 0.021 0.001 HIS a 530 PHE 0.015 0.001 PHE a 111 TYR 0.013 0.001 TYR l 329 ARG 0.010 0.000 ARG l 417 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12216 Ramachandran restraints generated. 6108 Oldfield, 0 Emsley, 6108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12216 Ramachandran restraints generated. 6108 Oldfield, 0 Emsley, 6108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 307 time to evaluate : 4.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 524 LYS cc_start: 0.9252 (mptt) cc_final: 0.8800 (tptt) REVERT: b 396 MET cc_start: 0.7775 (tmm) cc_final: 0.7574 (tmm) REVERT: b 524 LYS cc_start: 0.9160 (mmtt) cc_final: 0.8449 (tptm) REVERT: c 131 MET cc_start: 0.9063 (mmt) cc_final: 0.8706 (mmt) REVERT: d 130 MET cc_start: 0.9226 (mmt) cc_final: 0.8967 (mmt) REVERT: d 396 MET cc_start: 0.8054 (tmm) cc_final: 0.7829 (tmm) REVERT: d 524 LYS cc_start: 0.9182 (mmtt) cc_final: 0.8264 (tptm) REVERT: d 559 ILE cc_start: 0.9635 (OUTLIER) cc_final: 0.9399 (mm) REVERT: e 130 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8835 (mmm) REVERT: e 396 MET cc_start: 0.7785 (tmm) cc_final: 0.7525 (tmm) REVERT: e 447 MET cc_start: 0.8384 (tpt) cc_final: 0.7905 (tpt) REVERT: e 524 LYS cc_start: 0.9296 (mmtt) cc_final: 0.8713 (tptt) REVERT: f 73 MET cc_start: 0.8817 (mmt) cc_final: 0.8506 (mmt) REVERT: f 131 MET cc_start: 0.8876 (mmt) cc_final: 0.8551 (mmt) REVERT: f 396 MET cc_start: 0.8074 (tmm) cc_final: 0.7747 (tmm) REVERT: f 417 ARG cc_start: 0.8930 (ptp-110) cc_final: 0.8543 (ptm160) REVERT: f 524 LYS cc_start: 0.9284 (mmtt) cc_final: 0.8778 (tptt) REVERT: f 528 MET cc_start: 0.9467 (tmm) cc_final: 0.9239 (tmm) REVERT: g 453 MET cc_start: 0.8388 (mpp) cc_final: 0.7945 (ptt) REVERT: g 524 LYS cc_start: 0.9184 (mmtt) cc_final: 0.8917 (mmtt) REVERT: h 130 MET cc_start: 0.9222 (mmt) cc_final: 0.8767 (mmm) REVERT: h 524 LYS cc_start: 0.9188 (mmtt) cc_final: 0.8765 (tptt) REVERT: i 528 MET cc_start: 0.9380 (tmm) cc_final: 0.9107 (tmm) REVERT: j 130 MET cc_start: 0.9203 (mmt) cc_final: 0.8982 (mmm) REVERT: j 430 ASP cc_start: 0.8224 (m-30) cc_final: 0.7976 (p0) REVERT: j 528 MET cc_start: 0.9404 (tmm) cc_final: 0.9160 (tmm) REVERT: k 524 LYS cc_start: 0.9398 (mmtt) cc_final: 0.8926 (tptt) REVERT: l 130 MET cc_start: 0.9078 (mmm) cc_final: 0.8641 (mmm) REVERT: l 524 LYS cc_start: 0.9269 (mmtt) cc_final: 0.8718 (tptt) outliers start: 71 outliers final: 54 residues processed: 359 average time/residue: 0.4688 time to fit residues: 289.9873 Evaluate side-chains 363 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 307 time to evaluate : 4.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 110 LEU Chi-restraints excluded: chain a residue 377 VAL Chi-restraints excluded: chain a residue 482 HIS Chi-restraints excluded: chain a residue 536 GLU Chi-restraints excluded: chain a residue 569 TYR Chi-restraints excluded: chain b residue 130 MET Chi-restraints excluded: chain b residue 377 VAL Chi-restraints excluded: chain b residue 536 GLU Chi-restraints excluded: chain b residue 549 VAL Chi-restraints excluded: chain b residue 569 TYR Chi-restraints excluded: chain c residue 377 VAL Chi-restraints excluded: chain c residue 482 HIS Chi-restraints excluded: chain c residue 536 GLU Chi-restraints excluded: chain c residue 549 VAL Chi-restraints excluded: chain c residue 569 TYR Chi-restraints excluded: chain d residue 110 LEU Chi-restraints excluded: chain d residue 377 VAL Chi-restraints excluded: chain d residue 482 HIS Chi-restraints excluded: chain d residue 559 ILE Chi-restraints excluded: chain d residue 569 TYR Chi-restraints excluded: chain e residue 130 MET Chi-restraints excluded: chain e residue 377 VAL Chi-restraints excluded: chain e residue 482 HIS Chi-restraints excluded: chain e residue 569 TYR Chi-restraints excluded: chain f residue 110 LEU Chi-restraints excluded: chain f residue 362 ILE Chi-restraints excluded: chain f residue 377 VAL Chi-restraints excluded: chain f residue 482 HIS Chi-restraints excluded: chain f residue 536 GLU Chi-restraints excluded: chain f residue 549 VAL Chi-restraints excluded: chain f residue 569 TYR Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain g residue 377 VAL Chi-restraints excluded: chain g residue 482 HIS Chi-restraints excluded: chain g residue 569 TYR Chi-restraints excluded: chain h residue 110 LEU Chi-restraints excluded: chain h residue 377 VAL Chi-restraints excluded: chain h residue 482 HIS Chi-restraints excluded: chain h residue 569 TYR Chi-restraints excluded: chain i residue 377 VAL Chi-restraints excluded: chain i residue 482 HIS Chi-restraints excluded: chain i residue 536 GLU Chi-restraints excluded: chain i residue 569 TYR Chi-restraints excluded: chain j residue 135 VAL Chi-restraints excluded: chain j residue 377 VAL Chi-restraints excluded: chain j residue 549 VAL Chi-restraints excluded: chain j residue 569 TYR Chi-restraints excluded: chain k residue 110 LEU Chi-restraints excluded: chain k residue 377 VAL Chi-restraints excluded: chain k residue 549 VAL Chi-restraints excluded: chain k residue 569 TYR Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain l residue 377 VAL Chi-restraints excluded: chain l residue 482 HIS Chi-restraints excluded: chain l residue 549 VAL Chi-restraints excluded: chain l residue 569 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 536 optimal weight: 6.9990 chunk 565 optimal weight: 8.9990 chunk 515 optimal weight: 8.9990 chunk 549 optimal weight: 0.9990 chunk 564 optimal weight: 20.0000 chunk 330 optimal weight: 20.0000 chunk 239 optimal weight: 30.0000 chunk 431 optimal weight: 0.0370 chunk 168 optimal weight: 7.9990 chunk 496 optimal weight: 8.9990 chunk 519 optimal weight: 2.9990 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 367 GLN ** a 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 367 GLN ** f 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 558 ASN ** h 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 566 ASN ** j 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 367 GLN ** k 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 50712 Z= 0.190 Angle : 0.721 14.364 68448 Z= 0.370 Chirality : 0.043 0.236 7512 Planarity : 0.004 0.059 8976 Dihedral : 5.274 53.590 6768 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.72 % Allowed : 16.49 % Favored : 82.79 % Rotamer: Outliers : 1.19 % Allowed : 20.02 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.38 (0.11), residues: 6108 helix: 0.55 (0.10), residues: 2652 sheet: -0.42 (0.29), residues: 468 loop : -4.03 (0.10), residues: 2988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP c 576 HIS 0.017 0.001 HIS a 530 PHE 0.023 0.001 PHE d 111 TYR 0.011 0.001 TYR a 412 ARG 0.007 0.000 ARG d 474 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12216 Ramachandran restraints generated. 6108 Oldfield, 0 Emsley, 6108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12216 Ramachandran restraints generated. 6108 Oldfield, 0 Emsley, 6108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 310 time to evaluate : 4.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 367 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7488 (tm-30) REVERT: a 396 MET cc_start: 0.7752 (tmm) cc_final: 0.7422 (tmm) REVERT: a 524 LYS cc_start: 0.9179 (mptt) cc_final: 0.8762 (tptt) REVERT: b 396 MET cc_start: 0.7824 (tmm) cc_final: 0.7610 (tmm) REVERT: b 524 LYS cc_start: 0.9069 (mmtt) cc_final: 0.8423 (tptm) REVERT: c 131 MET cc_start: 0.9009 (mmt) cc_final: 0.8652 (mmt) REVERT: c 524 LYS cc_start: 0.9366 (mmtt) cc_final: 0.8709 (tptt) REVERT: d 130 MET cc_start: 0.9150 (mmt) cc_final: 0.8893 (mmt) REVERT: d 396 MET cc_start: 0.8083 (tmm) cc_final: 0.7846 (tmm) REVERT: d 559 ILE cc_start: 0.9607 (OUTLIER) cc_final: 0.9358 (mm) REVERT: e 396 MET cc_start: 0.7719 (tmm) cc_final: 0.7451 (tmm) REVERT: e 447 MET cc_start: 0.8419 (tpt) cc_final: 0.7903 (tpt) REVERT: e 524 LYS cc_start: 0.9177 (mmtt) cc_final: 0.8619 (tptt) REVERT: e 528 MET cc_start: 0.9307 (tmm) cc_final: 0.8915 (tmm) REVERT: f 73 MET cc_start: 0.8815 (mmt) cc_final: 0.8505 (mmt) REVERT: f 367 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: f 396 MET cc_start: 0.8024 (tmm) cc_final: 0.7675 (tmm) REVERT: f 417 ARG cc_start: 0.8959 (ptp-110) cc_final: 0.8577 (ptm160) REVERT: f 524 LYS cc_start: 0.9289 (mmtt) cc_final: 0.8751 (tptt) REVERT: f 528 MET cc_start: 0.9416 (tmm) cc_final: 0.9096 (tmm) REVERT: g 453 MET cc_start: 0.8323 (mpp) cc_final: 0.7836 (ptt) REVERT: g 524 LYS cc_start: 0.9132 (mmtt) cc_final: 0.8851 (mmtt) REVERT: h 130 MET cc_start: 0.9183 (mmt) cc_final: 0.8755 (mmm) REVERT: h 524 LYS cc_start: 0.9153 (mmtt) cc_final: 0.8698 (tptt) REVERT: i 528 MET cc_start: 0.9375 (tmm) cc_final: 0.9149 (tmm) REVERT: j 130 MET cc_start: 0.9199 (mmt) cc_final: 0.8987 (mmm) REVERT: j 528 MET cc_start: 0.9419 (tmm) cc_final: 0.9182 (tmm) REVERT: k 367 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: k 447 MET cc_start: 0.8459 (tmm) cc_final: 0.8086 (tmm) REVERT: k 524 LYS cc_start: 0.9314 (mmtt) cc_final: 0.8841 (tptt) REVERT: l 130 MET cc_start: 0.9060 (mmm) cc_final: 0.8659 (mmm) REVERT: l 524 LYS cc_start: 0.9220 (mmtt) cc_final: 0.8689 (tptt) outliers start: 65 outliers final: 53 residues processed: 357 average time/residue: 0.4771 time to fit residues: 290.1991 Evaluate side-chains 354 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 297 time to evaluate : 4.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 135 VAL Chi-restraints excluded: chain a residue 367 GLN Chi-restraints excluded: chain a residue 377 VAL Chi-restraints excluded: chain a residue 482 HIS Chi-restraints excluded: chain a residue 569 TYR Chi-restraints excluded: chain b residue 130 MET Chi-restraints excluded: chain b residue 377 VAL Chi-restraints excluded: chain b residue 536 GLU Chi-restraints excluded: chain b residue 549 VAL Chi-restraints excluded: chain b residue 569 TYR Chi-restraints excluded: chain c residue 377 VAL Chi-restraints excluded: chain c residue 482 HIS Chi-restraints excluded: chain c residue 549 VAL Chi-restraints excluded: chain c residue 569 TYR Chi-restraints excluded: chain d residue 110 LEU Chi-restraints excluded: chain d residue 377 VAL Chi-restraints excluded: chain d residue 482 HIS Chi-restraints excluded: chain d residue 559 ILE Chi-restraints excluded: chain d residue 569 TYR Chi-restraints excluded: chain e residue 130 MET Chi-restraints excluded: chain e residue 377 VAL Chi-restraints excluded: chain e residue 482 HIS Chi-restraints excluded: chain e residue 569 TYR Chi-restraints excluded: chain f residue 110 LEU Chi-restraints excluded: chain f residue 135 VAL Chi-restraints excluded: chain f residue 367 GLN Chi-restraints excluded: chain f residue 377 VAL Chi-restraints excluded: chain f residue 482 HIS Chi-restraints excluded: chain f residue 536 GLU Chi-restraints excluded: chain f residue 569 TYR Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain g residue 377 VAL Chi-restraints excluded: chain g residue 482 HIS Chi-restraints excluded: chain g residue 569 TYR Chi-restraints excluded: chain h residue 110 LEU Chi-restraints excluded: chain h residue 377 VAL Chi-restraints excluded: chain h residue 482 HIS Chi-restraints excluded: chain h residue 488 ASN Chi-restraints excluded: chain h residue 569 TYR Chi-restraints excluded: chain i residue 377 VAL Chi-restraints excluded: chain i residue 482 HIS Chi-restraints excluded: chain i residue 536 GLU Chi-restraints excluded: chain i residue 569 TYR Chi-restraints excluded: chain j residue 135 VAL Chi-restraints excluded: chain j residue 377 VAL Chi-restraints excluded: chain j residue 549 VAL Chi-restraints excluded: chain j residue 569 TYR Chi-restraints excluded: chain k residue 110 LEU Chi-restraints excluded: chain k residue 367 GLN Chi-restraints excluded: chain k residue 377 VAL Chi-restraints excluded: chain k residue 482 HIS Chi-restraints excluded: chain k residue 569 TYR Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain l residue 377 VAL Chi-restraints excluded: chain l residue 482 HIS Chi-restraints excluded: chain l residue 549 VAL Chi-restraints excluded: chain l residue 569 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 547 optimal weight: 10.0000 chunk 360 optimal weight: 9.9990 chunk 581 optimal weight: 8.9990 chunk 354 optimal weight: 0.0020 chunk 275 optimal weight: 2.9990 chunk 404 optimal weight: 0.3980 chunk 609 optimal weight: 8.9990 chunk 561 optimal weight: 50.0000 chunk 485 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 375 optimal weight: 50.0000 overall best weight: 3.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 367 GLN ** a 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 50712 Z= 0.189 Angle : 0.729 14.768 68448 Z= 0.372 Chirality : 0.044 0.236 7512 Planarity : 0.004 0.059 8976 Dihedral : 5.255 53.653 6768 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.70 % Allowed : 16.42 % Favored : 82.87 % Rotamer: Outliers : 1.06 % Allowed : 20.05 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.36 (0.11), residues: 6108 helix: 0.58 (0.11), residues: 2628 sheet: -0.38 (0.29), residues: 468 loop : -4.01 (0.10), residues: 3012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP c 576 HIS 0.023 0.001 HIS a 530 PHE 0.024 0.001 PHE d 111 TYR 0.011 0.001 TYR a 412 ARG 0.009 0.000 ARG g 474 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12216 Ramachandran restraints generated. 6108 Oldfield, 0 Emsley, 6108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12216 Ramachandran restraints generated. 6108 Oldfield, 0 Emsley, 6108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 298 time to evaluate : 4.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 367 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7726 (tm-30) REVERT: a 396 MET cc_start: 0.7879 (tmm) cc_final: 0.7501 (tmm) REVERT: a 524 LYS cc_start: 0.9199 (mptt) cc_final: 0.8776 (tptt) REVERT: b 396 MET cc_start: 0.7824 (tmm) cc_final: 0.7610 (tmm) REVERT: b 414 MET cc_start: 0.8361 (tpp) cc_final: 0.8147 (tpp) REVERT: b 524 LYS cc_start: 0.9067 (mmtt) cc_final: 0.8400 (tptm) REVERT: c 131 MET cc_start: 0.9007 (mmt) cc_final: 0.8660 (mmt) REVERT: c 524 LYS cc_start: 0.9336 (mmtt) cc_final: 0.8681 (tptt) REVERT: d 130 MET cc_start: 0.9149 (mmt) cc_final: 0.8896 (mmt) REVERT: d 396 MET cc_start: 0.8079 (tmm) cc_final: 0.7836 (tmm) REVERT: d 528 MET cc_start: 0.9280 (tmm) cc_final: 0.8840 (tmm) REVERT: d 559 ILE cc_start: 0.9551 (OUTLIER) cc_final: 0.9078 (mp) REVERT: e 396 MET cc_start: 0.7763 (tmm) cc_final: 0.7485 (tmm) REVERT: e 447 MET cc_start: 0.8390 (tpt) cc_final: 0.7848 (tpt) REVERT: e 524 LYS cc_start: 0.9163 (mmtt) cc_final: 0.8608 (tptt) REVERT: e 528 MET cc_start: 0.9319 (tmm) cc_final: 0.8937 (tmm) REVERT: f 73 MET cc_start: 0.8814 (mmt) cc_final: 0.8501 (mmt) REVERT: f 396 MET cc_start: 0.8019 (tmm) cc_final: 0.7664 (tmm) REVERT: f 417 ARG cc_start: 0.8952 (ptp-110) cc_final: 0.8580 (ptm160) REVERT: f 524 LYS cc_start: 0.9262 (mmtt) cc_final: 0.8752 (tptt) REVERT: f 528 MET cc_start: 0.9403 (tmm) cc_final: 0.9193 (tmm) REVERT: g 359 MET cc_start: 0.8402 (ppp) cc_final: 0.8141 (ppp) REVERT: g 453 MET cc_start: 0.8334 (mpp) cc_final: 0.7853 (ptt) REVERT: g 524 LYS cc_start: 0.9106 (mmtt) cc_final: 0.8819 (mmtt) REVERT: g 528 MET cc_start: 0.9313 (tmm) cc_final: 0.8969 (tmm) REVERT: h 130 MET cc_start: 0.9191 (mmt) cc_final: 0.8762 (mmm) REVERT: h 524 LYS cc_start: 0.9127 (mmtt) cc_final: 0.8667 (tptt) REVERT: i 528 MET cc_start: 0.9394 (tmm) cc_final: 0.9170 (tmm) REVERT: j 528 MET cc_start: 0.9450 (tmm) cc_final: 0.9211 (tmm) REVERT: k 447 MET cc_start: 0.8469 (tmm) cc_final: 0.8171 (tmm) REVERT: k 524 LYS cc_start: 0.9309 (mmtt) cc_final: 0.8828 (tptt) REVERT: l 130 MET cc_start: 0.9063 (mmm) cc_final: 0.8664 (mmm) REVERT: l 524 LYS cc_start: 0.9199 (mmtt) cc_final: 0.8632 (tptt) outliers start: 58 outliers final: 53 residues processed: 339 average time/residue: 0.4681 time to fit residues: 272.3196 Evaluate side-chains 351 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 296 time to evaluate : 4.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 135 VAL Chi-restraints excluded: chain a residue 367 GLN Chi-restraints excluded: chain a residue 377 VAL Chi-restraints excluded: chain a residue 482 HIS Chi-restraints excluded: chain a residue 569 TYR Chi-restraints excluded: chain b residue 130 MET Chi-restraints excluded: chain b residue 377 VAL Chi-restraints excluded: chain b residue 536 GLU Chi-restraints excluded: chain b residue 549 VAL Chi-restraints excluded: chain b residue 569 TYR Chi-restraints excluded: chain c residue 377 VAL Chi-restraints excluded: chain c residue 482 HIS Chi-restraints excluded: chain c residue 549 VAL Chi-restraints excluded: chain c residue 569 TYR Chi-restraints excluded: chain d residue 110 LEU Chi-restraints excluded: chain d residue 377 VAL Chi-restraints excluded: chain d residue 482 HIS Chi-restraints excluded: chain d residue 559 ILE Chi-restraints excluded: chain d residue 569 TYR Chi-restraints excluded: chain e residue 130 MET Chi-restraints excluded: chain e residue 377 VAL Chi-restraints excluded: chain e residue 482 HIS Chi-restraints excluded: chain e residue 569 TYR Chi-restraints excluded: chain f residue 110 LEU Chi-restraints excluded: chain f residue 135 VAL Chi-restraints excluded: chain f residue 377 VAL Chi-restraints excluded: chain f residue 482 HIS Chi-restraints excluded: chain f residue 536 GLU Chi-restraints excluded: chain f residue 569 TYR Chi-restraints excluded: chain g residue 377 VAL Chi-restraints excluded: chain g residue 482 HIS Chi-restraints excluded: chain g residue 569 TYR Chi-restraints excluded: chain h residue 110 LEU Chi-restraints excluded: chain h residue 377 VAL Chi-restraints excluded: chain h residue 482 HIS Chi-restraints excluded: chain h residue 488 ASN Chi-restraints excluded: chain h residue 569 TYR Chi-restraints excluded: chain i residue 377 VAL Chi-restraints excluded: chain i residue 482 HIS Chi-restraints excluded: chain i residue 536 GLU Chi-restraints excluded: chain i residue 569 TYR Chi-restraints excluded: chain j residue 135 VAL Chi-restraints excluded: chain j residue 377 VAL Chi-restraints excluded: chain j residue 549 VAL Chi-restraints excluded: chain j residue 569 TYR Chi-restraints excluded: chain k residue 110 LEU Chi-restraints excluded: chain k residue 377 VAL Chi-restraints excluded: chain k residue 482 HIS Chi-restraints excluded: chain k residue 549 VAL Chi-restraints excluded: chain k residue 569 TYR Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain l residue 377 VAL Chi-restraints excluded: chain l residue 482 HIS Chi-restraints excluded: chain l residue 549 VAL Chi-restraints excluded: chain l residue 569 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 297 optimal weight: 30.0000 chunk 385 optimal weight: 20.0000 chunk 517 optimal weight: 0.0370 chunk 148 optimal weight: 30.0000 chunk 447 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 486 optimal weight: 10.0000 chunk 203 optimal weight: 8.9990 chunk 499 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 overall best weight: 6.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 450 ASN ** i 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.071508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.060383 restraints weight = 420321.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.061021 restraints weight = 334958.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.061260 restraints weight = 282081.914| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 50712 Z= 0.216 Angle : 0.740 14.742 68448 Z= 0.378 Chirality : 0.044 0.235 7512 Planarity : 0.004 0.059 8976 Dihedral : 5.288 53.550 6768 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.70 % Allowed : 16.62 % Favored : 82.68 % Rotamer: Outliers : 1.10 % Allowed : 20.24 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.32 (0.11), residues: 6108 helix: 0.64 (0.11), residues: 2616 sheet: -0.38 (0.29), residues: 468 loop : -4.00 (0.10), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP c 576 HIS 0.022 0.001 HIS a 530 PHE 0.016 0.001 PHE d 111 TYR 0.013 0.001 TYR f 329 ARG 0.013 0.000 ARG l 474 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6999.72 seconds wall clock time: 124 minutes 27.29 seconds (7467.29 seconds total)