Starting phenix.real_space_refine (version: dev) on Thu Dec 22 14:25:47 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sya_25521/12_2022/7sya_25521.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sya_25521/12_2022/7sya_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_25521/12_2022/7sya_25521.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sya_25521/12_2022/7sya_25521.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sya_25521/12_2022/7sya_25521.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sya_25521/12_2022/7sya_25521.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "a PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 416": "OD1" <-> "OD2" Residue "c PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 416": "OD1" <-> "OD2" Residue "g PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 416": "OD1" <-> "OD2" Residue "k PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 27.00, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.08 Conformation dependent library (CDL) restraints added in 7.6 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: 1.71 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: 17.29 Time building geometry restraints manager: 21.80 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: 98.50 - 105.64: 881 105.64 - 112.79: 26509 112.79 - 119.94: 18168 119.94 - 127.08: 22400 127.08 - 134.23: 490 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 2.520 nonbonded pdb=" OD2 ASP h 573 " pdb=" NH1 ARG h 574 " model vdw 2.090 2.520 nonbonded pdb=" NE2 GLN f 126 " pdb=" O ARG g 330 " model vdw 2.191 2.520 nonbonded pdb=" NE2 GLN e 126 " pdb=" O ARG l 330 " model vdw 2.197 2.520 nonbonded pdb=" O LEU g 478 " pdb=" ND1 HIS g 482 " model vdw 2.211 2.520 ... (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 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 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. 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: 0.940 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: 9.290 Check model and map are aligned: 0.760 Convert atoms to be neutral: 0.430 Process input model: 120.640 Find NCS groups from input model: 3.400 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 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 : 15.83 Ramachandran Plot: Outliers : 0.75 % Allowed : 16.52 % Favored : 82.73 % Rotamer Outliers : 0.11 % 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 *********************** 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 : 6.340 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 339 average time/residue: 0.6001 time to fit residues: 343.9397 Evaluate side-chains 297 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 6.159 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.2522 ------------------------------------------------------------------------------- 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: 0.9980 chunk 463 optimal weight: 30.0000 chunk 257 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 chunk 312 optimal weight: 5.9990 chunk 247 optimal weight: 40.0000 chunk 479 optimal weight: 40.0000 chunk 185 optimal weight: 30.0000 chunk 291 optimal weight: 6.9990 chunk 357 optimal weight: 70.0000 chunk 555 optimal weight: 5.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 530 HIS ** a 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 482 HIS ** 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 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 450 ASN ** 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** ** k 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7361 moved from start: 0.0735 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= 0.205 Angle : 0.643 6.776 68448 Z= 0.340 Chirality : 0.042 0.182 7512 Planarity : 0.004 0.068 8976 Dihedral : 5.304 55.423 6768 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.75 % Allowed : 17.11 % Favored : 82.14 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.41 (0.10), residues: 2652 sheet: -0.55 (0.29), residues: 468 loop : -4.11 (0.09), residues: 2988 *********************** 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 337 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 305 time to evaluate : 6.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 14 residues processed: 324 average time/residue: 0.6023 time to fit residues: 331.9139 Evaluate side-chains 308 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 294 time to evaluate : 6.000 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.4601 time to fit residues: 20.1194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 308 optimal weight: 7.9990 chunk 172 optimal weight: 30.0000 chunk 462 optimal weight: 20.0000 chunk 378 optimal weight: 9.9990 chunk 153 optimal weight: 70.0000 chunk 556 optimal weight: 9.9990 chunk 601 optimal weight: 8.9990 chunk 495 optimal weight: 50.0000 chunk 552 optimal weight: 10.0000 chunk 189 optimal weight: 50.0000 chunk 446 optimal weight: 9.9990 overall best weight: 9.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 37 GLN a 480 HIS ** a 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 37 GLN ** b 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 530 HIS ** b 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 37 GLN ** 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 e 37 GLN ** e 482 HIS ** 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 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** i 450 ASN ** i 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 37 GLN ** j 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 37 GLN ** k 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 530 HIS l 558 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 50712 Z= 0.271 Angle : 0.674 8.926 68448 Z= 0.357 Chirality : 0.043 0.253 7512 Planarity : 0.005 0.061 8976 Dihedral : 5.374 54.256 6768 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.75 % Allowed : 17.31 % Favored : 81.94 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.53 (0.11), residues: 6108 helix: 0.44 (0.10), residues: 2652 sheet: -0.55 (0.29), residues: 468 loop : -4.11 (0.09), residues: 2988 *********************** 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 345 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 302 time to evaluate : 6.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 17 residues processed: 333 average time/residue: 0.5864 time to fit residues: 334.5109 Evaluate side-chains 315 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 298 time to evaluate : 5.965 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4436 time to fit residues: 22.1287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 550 optimal weight: 30.0000 chunk 418 optimal weight: 3.9990 chunk 288 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 265 optimal weight: 9.9990 chunk 373 optimal weight: 50.0000 chunk 558 optimal weight: 10.0000 chunk 591 optimal weight: 8.9990 chunk 291 optimal weight: 50.0000 chunk 529 optimal weight: 20.0000 chunk 159 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 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 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 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 558 ASN ** 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 367 GLN ** 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** ** 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 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 554 GLN l 480 HIS l 530 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 50712 Z= 0.234 Angle : 0.667 9.053 68448 Z= 0.351 Chirality : 0.043 0.185 7512 Planarity : 0.004 0.060 8976 Dihedral : 5.353 54.407 6768 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.75 % Allowed : 17.35 % Favored : 81.89 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.51 (0.11), residues: 6108 helix: 0.43 (0.10), residues: 2664 sheet: -0.52 (0.29), residues: 468 loop : -4.11 (0.09), residues: 2976 *********************** 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 412 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 309 time to evaluate : 6.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 29 residues processed: 396 average time/residue: 0.5718 time to fit residues: 391.4211 Evaluate side-chains 332 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 303 time to evaluate : 6.455 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.4566 time to fit residues: 33.7053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 492 optimal weight: 20.0000 chunk 335 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 440 optimal weight: 2.9990 chunk 244 optimal weight: 20.0000 chunk 504 optimal weight: 6.9990 chunk 408 optimal weight: 70.0000 chunk 0 optimal weight: 70.0000 chunk 302 optimal weight: 7.9990 chunk 530 optimal weight: 5.9990 chunk 149 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 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 480 HIS ** 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** e 480 HIS ** 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 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** ** h 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 558 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 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 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1619 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= 0.220 Angle : 0.674 9.020 68448 Z= 0.354 Chirality : 0.043 0.195 7512 Planarity : 0.004 0.059 8976 Dihedral : 5.330 54.606 6768 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.75 % Allowed : 17.19 % Favored : 82.06 % Rotamer Outliers : 1.43 % 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: -2.48 (0.11), residues: 6108 helix: 0.43 (0.10), residues: 2664 sheet: -0.47 (0.29), residues: 468 loop : -4.07 (0.09), residues: 2976 *********************** 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 389 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 311 time to evaluate : 6.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 22 residues processed: 378 average time/residue: 0.5895 time to fit residues: 388.2135 Evaluate side-chains 323 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 301 time to evaluate : 6.056 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.4688 time to fit residues: 27.3368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 199 optimal weight: 3.9990 chunk 532 optimal weight: 50.0000 chunk 116 optimal weight: 30.0000 chunk 347 optimal weight: 0.9980 chunk 146 optimal weight: 30.0000 chunk 592 optimal weight: 8.9990 chunk 491 optimal weight: 8.9990 chunk 274 optimal weight: 30.0000 chunk 49 optimal weight: 0.7980 chunk 195 optimal weight: 0.9980 chunk 310 optimal weight: 7.9990 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 558 ASN ** 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** ** 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 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 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 555 ASN ** 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** i 526 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1632 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= 0.176 Angle : 0.670 11.224 68448 Z= 0.349 Chirality : 0.042 0.198 7512 Planarity : 0.004 0.057 8976 Dihedral : 5.245 53.788 6768 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.75 % Allowed : 16.73 % Favored : 82.51 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.41 (0.11), residues: 6108 helix: 0.46 (0.10), residues: 2664 sheet: -0.38 (0.29), residues: 468 loop : -4.01 (0.10), residues: 2976 *********************** 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 366 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 307 time to evaluate : 6.609 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 21 residues processed: 358 average time/residue: 0.6054 time to fit residues: 370.3680 Evaluate side-chains 320 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 299 time to evaluate : 6.206 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.4840 time to fit residues: 26.8211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 570 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 337 optimal weight: 10.0000 chunk 432 optimal weight: 10.0000 chunk 335 optimal weight: 7.9990 chunk 498 optimal weight: 20.0000 chunk 330 optimal weight: 5.9990 chunk 589 optimal weight: 20.0000 chunk 369 optimal weight: 5.9990 chunk 359 optimal weight: 9.9990 chunk 272 optimal weight: 20.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 558 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 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 526 GLN ** d 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 482 HIS ** 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 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 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** ** i 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 526 GLN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1874 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= 0.245 Angle : 0.699 11.694 68448 Z= 0.364 Chirality : 0.043 0.212 7512 Planarity : 0.004 0.062 8976 Dihedral : 5.316 55.129 6768 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.74 % Allowed : 17.32 % Favored : 81.94 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.40 (0.11), residues: 6108 helix: 0.47 (0.10), residues: 2664 sheet: -0.36 (0.29), residues: 468 loop : -4.02 (0.10), residues: 2976 *********************** 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 358 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 306 time to evaluate : 6.400 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 28 residues processed: 346 average time/residue: 0.6046 time to fit residues: 358.1865 Evaluate side-chains 331 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 303 time to evaluate : 6.085 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.4607 time to fit residues: 32.0397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 364 optimal weight: 7.9990 chunk 235 optimal weight: 30.0000 chunk 352 optimal weight: 8.9990 chunk 177 optimal weight: 10.0000 chunk 115 optimal weight: 40.0000 chunk 114 optimal weight: 8.9990 chunk 375 optimal weight: 40.0000 chunk 401 optimal weight: 30.0000 chunk 291 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 463 optimal weight: 10.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 444 GLN ** 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 ** d 482 HIS ** 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 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 558 ASN ** 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 37 GLN ** 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** ** i 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 526 GLN ** 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 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2074 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= 0.262 Angle : 0.722 13.502 68448 Z= 0.375 Chirality : 0.044 0.219 7512 Planarity : 0.004 0.062 8976 Dihedral : 5.426 53.824 6768 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.74 % Allowed : 17.62 % Favored : 81.65 % Rotamer Outliers : 0.71 % 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: -2.44 (0.11), residues: 6108 helix: 0.44 (0.10), residues: 2664 sheet: -0.36 (0.29), residues: 468 loop : -4.04 (0.09), residues: 2976 *********************** 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 352 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 313 time to evaluate : 6.496 Fit side-chains outliers start: 39 outliers final: 21 residues processed: 343 average time/residue: 0.6078 time to fit residues: 359.6555 Evaluate side-chains 330 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 309 time to evaluate : 6.102 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.4554 time to fit residues: 26.2479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 536 optimal weight: 9.9990 chunk 565 optimal weight: 20.0000 chunk 515 optimal weight: 20.0000 chunk 549 optimal weight: 0.9990 chunk 564 optimal weight: 20.0000 chunk 330 optimal weight: 7.9990 chunk 239 optimal weight: 7.9990 chunk 431 optimal weight: 30.0000 chunk 168 optimal weight: 10.0000 chunk 496 optimal weight: 20.0000 chunk 519 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 554 GLN ** a 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 482 HIS ** 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 450 ASN ** f 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 482 HIS ** 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** i 526 GLN ** 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 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 50712 Z= 0.233 Angle : 0.715 16.023 68448 Z= 0.370 Chirality : 0.044 0.233 7512 Planarity : 0.004 0.062 8976 Dihedral : 5.422 55.440 6768 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.72 % Allowed : 17.42 % Favored : 81.86 % Rotamer Outliers : 0.44 % 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: -2.44 (0.11), residues: 6108 helix: 0.44 (0.10), residues: 2652 sheet: -0.31 (0.29), residues: 468 loop : -4.03 (0.10), residues: 2988 *********************** 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 340 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 316 time to evaluate : 6.266 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 333 average time/residue: 0.5966 time to fit residues: 341.4541 Evaluate side-chains 319 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 308 time to evaluate : 6.038 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4664 time to fit residues: 17.7441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 547 optimal weight: 3.9990 chunk 360 optimal weight: 6.9990 chunk 581 optimal weight: 30.0000 chunk 354 optimal weight: 7.9990 chunk 275 optimal weight: 20.0000 chunk 404 optimal weight: 0.7980 chunk 609 optimal weight: 6.9990 chunk 561 optimal weight: 60.0000 chunk 485 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 375 optimal weight: 50.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 482 HIS ** 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 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 482 HIS ** 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** ** i 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 526 GLN ** 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 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2137 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= 0.209 Angle : 0.717 18.715 68448 Z= 0.369 Chirality : 0.044 0.232 7512 Planarity : 0.004 0.062 8976 Dihedral : 5.377 54.721 6768 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.72 % Allowed : 17.26 % Favored : 82.02 % Rotamer Outliers : 0.24 % 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: 0.49 (0.10), residues: 2628 sheet: -0.24 (0.29), residues: 468 loop : -3.97 (0.10), residues: 3012 ********************** 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 322 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 309 time to evaluate : 6.065 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 319 average time/residue: 0.6672 time to fit residues: 365.7699 Evaluate side-chains 316 residues out of total 5460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 306 time to evaluate : 5.765 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4924 time to fit residues: 17.5090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 297 optimal weight: 40.0000 chunk 385 optimal weight: 0.0770 chunk 517 optimal weight: 7.9990 chunk 148 optimal weight: 4.9990 chunk 447 optimal weight: 5.9990 chunk 71 optimal weight: 40.0000 chunk 134 optimal weight: 9.9990 chunk 486 optimal weight: 7.9990 chunk 203 optimal weight: 9.9990 chunk 499 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 overall best weight: 3.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 482 HIS ** 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 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 482 HIS ** 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** i 526 GLN ** 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 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.071869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.060942 restraints weight = 420644.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.061612 restraints weight = 338302.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.061824 restraints weight = 286227.520| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2142 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= 0.188 Angle : 0.701 16.450 68448 Z= 0.360 Chirality : 0.043 0.236 7512 Planarity : 0.004 0.062 8976 Dihedral : 5.303 55.991 6768 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.70 % Allowed : 17.19 % Favored : 82.11 % Rotamer Outliers : 0.20 % 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: -2.31 (0.11), residues: 6108 helix: 0.53 (0.10), residues: 2628 sheet: -0.16 (0.29), residues: 468 loop : -3.93 (0.10), residues: 3012 =============================================================================== Job complete usr+sys time: 7938.47 seconds wall clock time: 146 minutes 47.37 seconds (8807.37 seconds total)