Starting phenix.real_space_refine (version: dev) on Fri Apr 8 04:52:56 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhs_12339/04_2022/7nhs_12339.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhs_12339/04_2022/7nhs_12339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhs_12339/04_2022/7nhs_12339.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhs_12339/04_2022/7nhs_12339.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhs_12339/04_2022/7nhs_12339.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhs_12339/04_2022/7nhs_12339.pdb" } resolution = 2.3 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= 0.007 sd= 0.102 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 GLU 64": "OE1" <-> "OE2" Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 675": "OE1" <-> "OE2" Residue "A TYR 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 600": "OE1" <-> "OE2" Residue "B PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 675": "OE1" <-> "OE2" Residue "B TYR 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 600": "OE1" <-> "OE2" Residue "C PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 675": "OE1" <-> "OE2" Residue "C TYR 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 215": "OD1" <-> "OD2" Residue "D PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 600": "OE1" <-> "OE2" Residue "D PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 675": "OE1" <-> "OE2" Residue "D TYR 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 64": "OE1" <-> "OE2" Residue "E TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 215": "OD1" <-> "OD2" Residue "E PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 600": "OE1" <-> "OE2" Residue "E PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 675": "OE1" <-> "OE2" Residue "E TYR 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 64": "OE1" <-> "OE2" Residue "F TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 215": "OD1" <-> "OD2" Residue "F PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 600": "OE1" <-> "OE2" Residue "F PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 675": "OE1" <-> "OE2" Residue "F TYR 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 215": "OD1" <-> "OD2" Residue "G PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 600": "OE1" <-> "OE2" Residue "G PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 675": "OE1" <-> "OE2" Residue "G TYR 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 64": "OE1" <-> "OE2" Residue "H TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 215": "OD1" <-> "OD2" Residue "H PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 600": "OE1" <-> "OE2" Residue "H PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 675": "OE1" <-> "OE2" Residue "H TYR 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 32240 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4030 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 21, 'TRANS': 499, 'PCIS': 1} Chain breaks: 3 Chain: "B" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4030 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 21, 'TRANS': 499, 'PCIS': 1} Chain breaks: 3 Chain: "C" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4030 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 21, 'TRANS': 499, 'PCIS': 1} Chain breaks: 3 Chain: "D" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4030 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 21, 'TRANS': 499, 'PCIS': 1} Chain breaks: 3 Chain: "E" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4030 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 21, 'TRANS': 499, 'PCIS': 1} Chain breaks: 3 Chain: "F" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4030 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 21, 'TRANS': 499, 'PCIS': 1} Chain breaks: 3 Chain: "G" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4030 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 21, 'TRANS': 499, 'PCIS': 1} Chain breaks: 3 Chain: "H" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4030 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 21, 'TRANS': 499, 'PCIS': 1} Chain breaks: 3 Time building chain proxies: 18.04, per 1000 atoms: 0.56 Number of scatterers: 32240 At special positions: 0 Unit cell: (159.168, 159.997, 137.614, 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 104 16.00 O 6048 8.00 N 5416 7.00 C 20672 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: 13.12 Conformation dependent library (CDL) restraints added in 5.3 seconds 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7712 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 32 sheets defined 47.3% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 18 through 29 Processing helix chain 'A' and resid 29 through 51 Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.553A pdb=" N ALA A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 107 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 208 through 219 Processing helix chain 'A' and resid 240 through 260 removed outlier: 3.747A pdb=" N SER A 245 " --> pdb=" O PRO A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 452 Processing helix chain 'A' and resid 457 through 464 removed outlier: 4.186A pdb=" N LEU A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 501 Processing helix chain 'A' and resid 504 through 522 removed outlier: 3.618A pdb=" N MET A 522 " --> pdb=" O HIS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 553 Processing helix chain 'A' and resid 569 through 575 Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 591 through 595 Processing helix chain 'A' and resid 615 through 621 removed outlier: 3.523A pdb=" N MET A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 636 removed outlier: 4.367A pdb=" N GLU A 626 " --> pdb=" O HIS A 622 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN A 634 " --> pdb=" O ASN A 630 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A 635 " --> pdb=" O TRP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 656 Processing helix chain 'A' and resid 672 through 686 Processing helix chain 'A' and resid 701 through 708 removed outlier: 3.659A pdb=" N TYR A 705 " --> pdb=" O LYS A 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 29 Processing helix chain 'B' and resid 29 through 51 Processing helix chain 'B' and resid 86 through 94 removed outlier: 3.553A pdb=" N ALA B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 107 Processing helix chain 'B' and resid 120 through 128 Processing helix chain 'B' and resid 208 through 219 Processing helix chain 'B' and resid 240 through 260 removed outlier: 3.748A pdb=" N SER B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 452 Processing helix chain 'B' and resid 457 through 464 removed outlier: 4.185A pdb=" N LEU B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 501 Processing helix chain 'B' and resid 504 through 522 removed outlier: 3.618A pdb=" N MET B 522 " --> pdb=" O HIS B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 553 Processing helix chain 'B' and resid 569 through 575 Processing helix chain 'B' and resid 581 through 588 Processing helix chain 'B' and resid 591 through 595 Processing helix chain 'B' and resid 615 through 621 removed outlier: 3.524A pdb=" N MET B 621 " --> pdb=" O ALA B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 636 removed outlier: 4.367A pdb=" N GLU B 626 " --> pdb=" O HIS B 622 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN B 634 " --> pdb=" O ASN B 630 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 656 Processing helix chain 'B' and resid 672 through 686 Processing helix chain 'B' and resid 701 through 708 removed outlier: 3.660A pdb=" N TYR B 705 " --> pdb=" O LYS B 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 29 Processing helix chain 'C' and resid 29 through 51 Processing helix chain 'C' and resid 86 through 94 removed outlier: 3.553A pdb=" N ALA C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 107 Processing helix chain 'C' and resid 120 through 128 Processing helix chain 'C' and resid 208 through 219 Processing helix chain 'C' and resid 240 through 260 removed outlier: 3.749A pdb=" N SER C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 452 Processing helix chain 'C' and resid 457 through 464 removed outlier: 4.185A pdb=" N LEU C 461 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE C 464 " --> pdb=" O GLN C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 501 Processing helix chain 'C' and resid 504 through 522 removed outlier: 3.618A pdb=" N MET C 522 " --> pdb=" O HIS C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 553 Processing helix chain 'C' and resid 569 through 575 Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 591 through 595 Processing helix chain 'C' and resid 615 through 621 removed outlier: 3.523A pdb=" N MET C 621 " --> pdb=" O ALA C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 636 removed outlier: 4.367A pdb=" N GLU C 626 " --> pdb=" O HIS C 622 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN C 634 " --> pdb=" O ASN C 630 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN C 635 " --> pdb=" O TRP C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 656 Processing helix chain 'C' and resid 672 through 686 Processing helix chain 'C' and resid 701 through 708 removed outlier: 3.660A pdb=" N TYR C 705 " --> pdb=" O LYS C 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 29 Processing helix chain 'D' and resid 29 through 51 Processing helix chain 'D' and resid 86 through 94 removed outlier: 3.553A pdb=" N ALA D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 107 Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 208 through 219 Processing helix chain 'D' and resid 240 through 260 removed outlier: 3.748A pdb=" N SER D 245 " --> pdb=" O PRO D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 452 Processing helix chain 'D' and resid 457 through 464 removed outlier: 4.185A pdb=" N LEU D 461 " --> pdb=" O SER D 457 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE D 464 " --> pdb=" O GLN D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 501 Processing helix chain 'D' and resid 504 through 522 removed outlier: 3.618A pdb=" N MET D 522 " --> pdb=" O HIS D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 553 Processing helix chain 'D' and resid 569 through 575 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 591 through 595 Processing helix chain 'D' and resid 615 through 621 removed outlier: 3.523A pdb=" N MET D 621 " --> pdb=" O ALA D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 636 removed outlier: 4.367A pdb=" N GLU D 626 " --> pdb=" O HIS D 622 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN D 634 " --> pdb=" O ASN D 630 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 656 Processing helix chain 'D' and resid 672 through 686 Processing helix chain 'D' and resid 701 through 708 removed outlier: 3.660A pdb=" N TYR D 705 " --> pdb=" O LYS D 701 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 29 Processing helix chain 'E' and resid 29 through 51 Processing helix chain 'E' and resid 86 through 94 removed outlier: 3.553A pdb=" N ALA E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 107 Processing helix chain 'E' and resid 120 through 128 Processing helix chain 'E' and resid 208 through 219 Processing helix chain 'E' and resid 240 through 260 removed outlier: 3.747A pdb=" N SER E 245 " --> pdb=" O PRO E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 452 Processing helix chain 'E' and resid 457 through 464 removed outlier: 4.186A pdb=" N LEU E 461 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE E 464 " --> pdb=" O GLN E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 501 Processing helix chain 'E' and resid 504 through 522 removed outlier: 3.617A pdb=" N MET E 522 " --> pdb=" O HIS E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 553 Processing helix chain 'E' and resid 569 through 575 Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 591 through 595 Processing helix chain 'E' and resid 615 through 621 removed outlier: 3.523A pdb=" N MET E 621 " --> pdb=" O ALA E 617 " (cutoff:3.500A) Processing helix chain 'E' and resid 622 through 636 removed outlier: 4.366A pdb=" N GLU E 626 " --> pdb=" O HIS E 622 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN E 634 " --> pdb=" O ASN E 630 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN E 635 " --> pdb=" O TRP E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 656 Processing helix chain 'E' and resid 672 through 686 Processing helix chain 'E' and resid 701 through 708 removed outlier: 3.660A pdb=" N TYR E 705 " --> pdb=" O LYS E 701 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 29 Processing helix chain 'F' and resid 29 through 51 Processing helix chain 'F' and resid 86 through 94 removed outlier: 3.554A pdb=" N ALA F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 107 Processing helix chain 'F' and resid 120 through 128 Processing helix chain 'F' and resid 208 through 219 Processing helix chain 'F' and resid 240 through 260 removed outlier: 3.748A pdb=" N SER F 245 " --> pdb=" O PRO F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 452 Processing helix chain 'F' and resid 457 through 464 removed outlier: 4.186A pdb=" N LEU F 461 " --> pdb=" O SER F 457 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE F 464 " --> pdb=" O GLN F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 501 Processing helix chain 'F' and resid 504 through 522 removed outlier: 3.618A pdb=" N MET F 522 " --> pdb=" O HIS F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 539 through 553 Processing helix chain 'F' and resid 569 through 575 Processing helix chain 'F' and resid 581 through 588 Processing helix chain 'F' and resid 591 through 595 Processing helix chain 'F' and resid 615 through 621 removed outlier: 3.523A pdb=" N MET F 621 " --> pdb=" O ALA F 617 " (cutoff:3.500A) Processing helix chain 'F' and resid 622 through 636 removed outlier: 4.367A pdb=" N GLU F 626 " --> pdb=" O HIS F 622 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN F 634 " --> pdb=" O ASN F 630 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 656 Processing helix chain 'F' and resid 672 through 686 Processing helix chain 'F' and resid 701 through 708 removed outlier: 3.660A pdb=" N TYR F 705 " --> pdb=" O LYS F 701 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 29 Processing helix chain 'G' and resid 29 through 51 Processing helix chain 'G' and resid 86 through 94 removed outlier: 3.554A pdb=" N ALA G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 208 through 219 Processing helix chain 'G' and resid 240 through 260 removed outlier: 3.748A pdb=" N SER G 245 " --> pdb=" O PRO G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 452 Processing helix chain 'G' and resid 457 through 464 removed outlier: 4.185A pdb=" N LEU G 461 " --> pdb=" O SER G 457 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE G 464 " --> pdb=" O GLN G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 501 Processing helix chain 'G' and resid 504 through 522 removed outlier: 3.618A pdb=" N MET G 522 " --> pdb=" O HIS G 518 " (cutoff:3.500A) Processing helix chain 'G' and resid 539 through 553 Processing helix chain 'G' and resid 569 through 575 Processing helix chain 'G' and resid 581 through 588 Processing helix chain 'G' and resid 591 through 595 Processing helix chain 'G' and resid 615 through 621 removed outlier: 3.522A pdb=" N MET G 621 " --> pdb=" O ALA G 617 " (cutoff:3.500A) Processing helix chain 'G' and resid 622 through 636 removed outlier: 4.367A pdb=" N GLU G 626 " --> pdb=" O HIS G 622 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN G 634 " --> pdb=" O ASN G 630 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN G 635 " --> pdb=" O TRP G 631 " (cutoff:3.500A) Processing helix chain 'G' and resid 650 through 656 Processing helix chain 'G' and resid 672 through 686 Processing helix chain 'G' and resid 701 through 708 removed outlier: 3.660A pdb=" N TYR G 705 " --> pdb=" O LYS G 701 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 29 Processing helix chain 'H' and resid 29 through 51 Processing helix chain 'H' and resid 86 through 94 removed outlier: 3.553A pdb=" N ALA H 91 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 Processing helix chain 'H' and resid 120 through 128 Processing helix chain 'H' and resid 208 through 219 Processing helix chain 'H' and resid 240 through 260 removed outlier: 3.747A pdb=" N SER H 245 " --> pdb=" O PRO H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 425 through 452 Processing helix chain 'H' and resid 457 through 464 removed outlier: 4.185A pdb=" N LEU H 461 " --> pdb=" O SER H 457 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE H 464 " --> pdb=" O GLN H 460 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 501 Processing helix chain 'H' and resid 504 through 522 removed outlier: 3.618A pdb=" N MET H 522 " --> pdb=" O HIS H 518 " (cutoff:3.500A) Processing helix chain 'H' and resid 539 through 553 Processing helix chain 'H' and resid 569 through 575 Processing helix chain 'H' and resid 581 through 588 Processing helix chain 'H' and resid 591 through 595 Processing helix chain 'H' and resid 615 through 621 removed outlier: 3.523A pdb=" N MET H 621 " --> pdb=" O ALA H 617 " (cutoff:3.500A) Processing helix chain 'H' and resid 622 through 636 removed outlier: 4.367A pdb=" N GLU H 626 " --> pdb=" O HIS H 622 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN H 634 " --> pdb=" O ASN H 630 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN H 635 " --> pdb=" O TRP H 631 " (cutoff:3.500A) Processing helix chain 'H' and resid 650 through 656 Processing helix chain 'H' and resid 672 through 686 Processing helix chain 'H' and resid 701 through 708 removed outlier: 3.660A pdb=" N TYR H 705 " --> pdb=" O LYS H 701 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 223 removed outlier: 6.874A pdb=" N GLU A 56 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL A 416 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ASP A 58 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASN A 414 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 60 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 141 removed outlier: 7.398A pdb=" N ASN A 134 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE A 194 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU A 190 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU A 140 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER A 188 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 468 through 473 removed outlier: 6.592A pdb=" N CYS A 693 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA A 470 " --> pdb=" O CYS A 693 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N CYS A 662 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE A 694 " --> pdb=" O CYS A 662 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 664 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ASN A 696 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA A 666 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 698 " --> pdb=" O ALA A 666 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY A 533 " --> pdb=" O THR A 643 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL A 558 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE A 607 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE A 560 " --> pdb=" O ILE A 607 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 220 through 223 removed outlier: 6.873A pdb=" N GLU B 56 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B 416 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASP B 58 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASN B 414 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU B 60 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AA7, first strand: chain 'B' and resid 134 through 141 removed outlier: 7.398A pdb=" N ASN B 134 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE B 194 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU B 190 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU B 140 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER B 188 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 468 through 473 removed outlier: 6.592A pdb=" N CYS B 693 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA B 470 " --> pdb=" O CYS B 693 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N CYS B 662 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE B 694 " --> pdb=" O CYS B 662 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU B 664 " --> pdb=" O ILE B 694 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ASN B 696 " --> pdb=" O LEU B 664 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA B 666 " --> pdb=" O ASN B 696 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 698 " --> pdb=" O ALA B 666 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY B 533 " --> pdb=" O THR B 643 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL B 558 " --> pdb=" O ASP B 605 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE B 607 " --> pdb=" O VAL B 558 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE B 560 " --> pdb=" O ILE B 607 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 220 through 223 removed outlier: 8.447A pdb=" N ILE C 54 " --> pdb=" O ASP C 418 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ASP C 418 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU C 56 " --> pdb=" O VAL C 416 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL C 416 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ASP C 58 " --> pdb=" O ASN C 414 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASN C 414 " --> pdb=" O ASP C 58 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU C 60 " --> pdb=" O ILE C 412 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 110 through 114 Processing sheet with id=AB2, first strand: chain 'C' and resid 134 through 141 removed outlier: 7.398A pdb=" N ASN C 134 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE C 194 " --> pdb=" O ASN C 134 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU C 190 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU C 140 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER C 188 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 468 through 473 removed outlier: 6.591A pdb=" N CYS C 693 " --> pdb=" O VAL C 468 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA C 470 " --> pdb=" O CYS C 693 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N CYS C 662 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE C 694 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU C 664 " --> pdb=" O ILE C 694 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ASN C 696 " --> pdb=" O LEU C 664 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA C 666 " --> pdb=" O ASN C 696 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL C 698 " --> pdb=" O ALA C 666 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY C 533 " --> pdb=" O THR C 643 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL C 558 " --> pdb=" O ASP C 605 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE C 607 " --> pdb=" O VAL C 558 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE C 560 " --> pdb=" O ILE C 607 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 220 through 223 removed outlier: 6.874A pdb=" N GLU D 56 " --> pdb=" O VAL D 416 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL D 416 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASP D 58 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASN D 414 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU D 60 " --> pdb=" O ILE D 412 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 110 through 114 Processing sheet with id=AB6, first strand: chain 'D' and resid 134 through 141 removed outlier: 7.399A pdb=" N ASN D 134 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE D 194 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU D 190 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU D 140 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER D 188 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 468 through 473 removed outlier: 6.592A pdb=" N CYS D 693 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA D 470 " --> pdb=" O CYS D 693 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N CYS D 662 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE D 694 " --> pdb=" O CYS D 662 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU D 664 " --> pdb=" O ILE D 694 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ASN D 696 " --> pdb=" O LEU D 664 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA D 666 " --> pdb=" O ASN D 696 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL D 698 " --> pdb=" O ALA D 666 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY D 533 " --> pdb=" O THR D 643 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL D 558 " --> pdb=" O ASP D 605 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE D 607 " --> pdb=" O VAL D 558 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N PHE D 560 " --> pdb=" O ILE D 607 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 220 through 223 removed outlier: 6.874A pdb=" N GLU E 56 " --> pdb=" O VAL E 416 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL E 416 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ASP E 58 " --> pdb=" O ASN E 414 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ASN E 414 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU E 60 " --> pdb=" O ILE E 412 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 110 through 114 Processing sheet with id=AC1, first strand: chain 'E' and resid 134 through 141 removed outlier: 7.399A pdb=" N ASN E 134 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ILE E 194 " --> pdb=" O ASN E 134 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU E 190 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU E 140 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER E 188 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 468 through 473 removed outlier: 6.592A pdb=" N CYS E 693 " --> pdb=" O VAL E 468 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA E 470 " --> pdb=" O CYS E 693 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N CYS E 662 " --> pdb=" O GLY E 692 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE E 694 " --> pdb=" O CYS E 662 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU E 664 " --> pdb=" O ILE E 694 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ASN E 696 " --> pdb=" O LEU E 664 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA E 666 " --> pdb=" O ASN E 696 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL E 698 " --> pdb=" O ALA E 666 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY E 533 " --> pdb=" O THR E 643 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL E 558 " --> pdb=" O ASP E 605 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE E 607 " --> pdb=" O VAL E 558 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE E 560 " --> pdb=" O ILE E 607 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 220 through 223 removed outlier: 6.874A pdb=" N GLU F 56 " --> pdb=" O VAL F 416 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL F 416 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASP F 58 " --> pdb=" O ASN F 414 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASN F 414 " --> pdb=" O ASP F 58 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU F 60 " --> pdb=" O ILE F 412 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 110 through 114 Processing sheet with id=AC5, first strand: chain 'F' and resid 134 through 141 removed outlier: 7.398A pdb=" N ASN F 134 " --> pdb=" O ILE F 194 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE F 194 " --> pdb=" O ASN F 134 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU F 190 " --> pdb=" O THR F 138 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU F 140 " --> pdb=" O SER F 188 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER F 188 " --> pdb=" O LEU F 140 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 468 through 473 removed outlier: 6.592A pdb=" N CYS F 693 " --> pdb=" O VAL F 468 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA F 470 " --> pdb=" O CYS F 693 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N CYS F 662 " --> pdb=" O GLY F 692 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE F 694 " --> pdb=" O CYS F 662 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU F 664 " --> pdb=" O ILE F 694 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ASN F 696 " --> pdb=" O LEU F 664 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA F 666 " --> pdb=" O ASN F 696 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL F 698 " --> pdb=" O ALA F 666 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY F 533 " --> pdb=" O THR F 643 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL F 558 " --> pdb=" O ASP F 605 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE F 607 " --> pdb=" O VAL F 558 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE F 560 " --> pdb=" O ILE F 607 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 220 through 223 removed outlier: 6.873A pdb=" N GLU G 56 " --> pdb=" O VAL G 416 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL G 416 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASP G 58 " --> pdb=" O ASN G 414 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASN G 414 " --> pdb=" O ASP G 58 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU G 60 " --> pdb=" O ILE G 412 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 110 through 114 Processing sheet with id=AC9, first strand: chain 'G' and resid 134 through 141 removed outlier: 7.399A pdb=" N ASN G 134 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE G 194 " --> pdb=" O ASN G 134 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU G 190 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU G 140 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER G 188 " --> pdb=" O LEU G 140 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 468 through 473 removed outlier: 6.591A pdb=" N CYS G 693 " --> pdb=" O VAL G 468 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA G 470 " --> pdb=" O CYS G 693 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N CYS G 662 " --> pdb=" O GLY G 692 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE G 694 " --> pdb=" O CYS G 662 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU G 664 " --> pdb=" O ILE G 694 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ASN G 696 " --> pdb=" O LEU G 664 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA G 666 " --> pdb=" O ASN G 696 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL G 698 " --> pdb=" O ALA G 666 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY G 533 " --> pdb=" O THR G 643 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL G 558 " --> pdb=" O ASP G 605 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE G 607 " --> pdb=" O VAL G 558 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N PHE G 560 " --> pdb=" O ILE G 607 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 220 through 223 removed outlier: 6.874A pdb=" N GLU H 56 " --> pdb=" O VAL H 416 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL H 416 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASP H 58 " --> pdb=" O ASN H 414 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASN H 414 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU H 60 " --> pdb=" O ILE H 412 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 110 through 114 Processing sheet with id=AD4, first strand: chain 'H' and resid 134 through 141 removed outlier: 7.399A pdb=" N ASN H 134 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE H 194 " --> pdb=" O ASN H 134 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU H 190 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU H 140 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER H 188 " --> pdb=" O LEU H 140 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 468 through 473 removed outlier: 6.591A pdb=" N CYS H 693 " --> pdb=" O VAL H 468 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA H 470 " --> pdb=" O CYS H 693 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N CYS H 662 " --> pdb=" O GLY H 692 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE H 694 " --> pdb=" O CYS H 662 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU H 664 " --> pdb=" O ILE H 694 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ASN H 696 " --> pdb=" O LEU H 664 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA H 666 " --> pdb=" O ASN H 696 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL H 698 " --> pdb=" O ALA H 666 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY H 533 " --> pdb=" O THR H 643 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL H 558 " --> pdb=" O ASP H 605 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE H 607 " --> pdb=" O VAL H 558 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N PHE H 560 " --> pdb=" O ILE H 607 " (cutoff:3.500A) 1704 hydrogen bonds defined for protein. 4995 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.30 Time building geometry restraints manager: 14.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10536 1.34 - 1.46: 6209 1.46 - 1.58: 15815 1.58 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 32752 Sorted by residual: bond pdb=" C PHE A 117 " pdb=" N PRO A 118 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.11e+00 bond pdb=" C PHE B 117 " pdb=" N PRO B 118 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.11e+00 bond pdb=" C PHE D 117 " pdb=" N PRO D 118 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.09e+00 bond pdb=" C PHE C 117 " pdb=" N PRO C 118 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.06e+00 bond pdb=" C PHE G 117 " pdb=" N PRO G 118 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.05e+00 ... (remaining 32747 not shown) Histogram of bond angle deviations from ideal: 100.72 - 107.38: 986 107.38 - 114.03: 19321 114.03 - 120.69: 13308 120.69 - 127.35: 10507 127.35 - 134.01: 254 Bond angle restraints: 44376 Sorted by residual: angle pdb=" N ILE D 260 " pdb=" CA ILE D 260 " pdb=" C ILE D 260 " ideal model delta sigma weight residual 112.80 109.37 3.43 1.15e+00 7.56e-01 8.92e+00 angle pdb=" N ILE A 260 " pdb=" CA ILE A 260 " pdb=" C ILE A 260 " ideal model delta sigma weight residual 112.80 109.37 3.43 1.15e+00 7.56e-01 8.88e+00 angle pdb=" N ILE E 260 " pdb=" CA ILE E 260 " pdb=" C ILE E 260 " ideal model delta sigma weight residual 112.80 109.38 3.42 1.15e+00 7.56e-01 8.84e+00 angle pdb=" N ILE B 260 " pdb=" CA ILE B 260 " pdb=" C ILE B 260 " ideal model delta sigma weight residual 112.80 109.38 3.42 1.15e+00 7.56e-01 8.82e+00 angle pdb=" N ILE F 260 " pdb=" CA ILE F 260 " pdb=" C ILE F 260 " ideal model delta sigma weight residual 112.80 109.38 3.42 1.15e+00 7.56e-01 8.82e+00 ... (remaining 44371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 19216 17.62 - 35.25: 520 35.25 - 52.87: 136 52.87 - 70.49: 32 70.49 - 88.12: 8 Dihedral angle restraints: 19912 sinusoidal: 7912 harmonic: 12000 Sorted by residual: dihedral pdb=" CA HIS G 576 " pdb=" C HIS G 576 " pdb=" N LYS G 577 " pdb=" CA LYS G 577 " ideal model delta harmonic sigma weight residual 180.00 154.12 25.88 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA HIS A 576 " pdb=" C HIS A 576 " pdb=" N LYS A 577 " pdb=" CA LYS A 577 " ideal model delta harmonic sigma weight residual 180.00 154.16 25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA HIS H 576 " pdb=" C HIS H 576 " pdb=" N LYS H 577 " pdb=" CA LYS H 577 " ideal model delta harmonic sigma weight residual 180.00 154.17 25.83 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 19909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3274 0.027 - 0.055: 1210 0.055 - 0.082: 355 0.082 - 0.110: 324 0.110 - 0.137: 133 Chirality restraints: 5296 Sorted by residual: chirality pdb=" CA ILE C 167 " pdb=" N ILE C 167 " pdb=" C ILE C 167 " pdb=" CB ILE C 167 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE E 167 " pdb=" N ILE E 167 " pdb=" C ILE E 167 " pdb=" CB ILE E 167 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA ILE H 167 " pdb=" N ILE H 167 " pdb=" C ILE H 167 " pdb=" CB ILE H 167 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 5293 not shown) Planarity restraints: 5640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 535 " 0.013 5.00e-02 4.00e+02 1.97e-02 6.22e-01 pdb=" N PRO E 536 " -0.034 5.00e-02 4.00e+02 pdb=" CA PRO E 536 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO E 536 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 535 " 0.013 5.00e-02 4.00e+02 1.96e-02 6.16e-01 pdb=" N PRO F 536 " -0.034 5.00e-02 4.00e+02 pdb=" CA PRO F 536 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO F 536 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 535 " 0.013 5.00e-02 4.00e+02 1.96e-02 6.15e-01 pdb=" N PRO C 536 " -0.034 5.00e-02 4.00e+02 pdb=" CA PRO C 536 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO C 536 " 0.011 5.00e-02 4.00e+02 ... (remaining 5637 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 8643 2.81 - 3.33: 31251 3.33 - 3.85: 53955 3.85 - 4.38: 65462 4.38 - 4.90: 107238 Nonbonded interactions: 266549 Sorted by model distance: nonbonded pdb=" O ILE B 551 " pdb=" OG1 THR B 554 " model vdw 2.284 2.440 nonbonded pdb=" O ILE G 551 " pdb=" OG1 THR G 554 " model vdw 2.284 2.440 nonbonded pdb=" O ILE D 551 " pdb=" OG1 THR D 554 " model vdw 2.284 2.440 nonbonded pdb=" O ILE H 551 " pdb=" OG1 THR H 554 " model vdw 2.284 2.440 nonbonded pdb=" O ILE C 551 " pdb=" OG1 THR C 554 " model vdw 2.285 2.440 ... (remaining 266544 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' } 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 104 5.16 5 C 20672 2.51 5 N 5416 2.21 5 O 6048 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 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: 0.030 Extract box with map and model: 13.730 Check model and map are aligned: 0.430 Convert atoms to be neutral: 0.240 Process input model: 83.940 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:14.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 32752 Z= 0.118 Angle : 0.479 7.433 44376 Z= 0.267 Chirality : 0.041 0.137 5296 Planarity : 0.002 0.020 5640 Dihedral : 9.506 88.117 12200 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.11), residues: 4112 helix: -1.53 (0.09), residues: 1864 sheet: -0.15 (0.18), residues: 696 loop : -2.10 (0.12), residues: 1552 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 661 time to evaluate : 4.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 3 residues processed: 661 average time/residue: 1.2473 time to fit residues: 993.2550 Evaluate side-chains 442 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 439 time to evaluate : 3.740 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.3099 time to fit residues: 6.7654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 351 optimal weight: 0.0570 chunk 315 optimal weight: 3.9990 chunk 174 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 212 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 326 optimal weight: 20.0000 chunk 126 optimal weight: 5.9990 chunk 198 optimal weight: 0.5980 chunk 242 optimal weight: 1.9990 chunk 377 optimal weight: 5.9990 overall best weight: 1.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS A 173 GLN A 206 GLN A 254 ASN A 571 HIS A 622 HIS A 671 ASN A 710 HIS B 29 HIS B 173 GLN B 206 GLN B 254 ASN B 571 HIS B 671 ASN B 710 HIS C 29 HIS C 173 GLN C 206 GLN C 254 ASN C 571 HIS C 622 HIS C 671 ASN C 710 HIS D 29 HIS D 173 GLN D 254 ASN D 671 ASN D 710 HIS E 29 HIS E 173 GLN E 254 ASN E 571 HIS E 611 GLN E 622 HIS E 671 ASN E 710 HIS F 29 HIS F 173 GLN F 254 ASN F 571 HIS F 671 ASN F 710 HIS G 29 HIS G 173 GLN G 206 GLN G 254 ASN G 571 HIS G 671 ASN G 710 HIS H 29 HIS H 173 GLN H 206 GLN H 254 ASN H 571 HIS H 671 ASN H 710 HIS Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 32752 Z= 0.211 Angle : 0.571 8.492 44376 Z= 0.296 Chirality : 0.044 0.195 5296 Planarity : 0.004 0.043 5640 Dihedral : 4.342 28.194 4456 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.12), residues: 4112 helix: 0.61 (0.11), residues: 1904 sheet: 0.42 (0.18), residues: 696 loop : -1.45 (0.14), residues: 1512 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 485 time to evaluate : 3.508 Fit side-chains revert: symmetry clash outliers start: 79 outliers final: 23 residues processed: 532 average time/residue: 1.1842 time to fit residues: 768.3546 Evaluate side-chains 436 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 413 time to evaluate : 4.033 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 16 residues processed: 10 average time/residue: 0.3589 time to fit residues: 11.6432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 209 optimal weight: 0.0060 chunk 117 optimal weight: 8.9990 chunk 314 optimal weight: 0.9980 chunk 257 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 378 optimal weight: 6.9990 chunk 408 optimal weight: 1.9990 chunk 337 optimal weight: 0.9990 chunk 375 optimal weight: 0.4980 chunk 129 optimal weight: 6.9990 chunk 303 optimal weight: 2.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN H 467 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 32752 Z= 0.174 Angle : 0.541 7.582 44376 Z= 0.278 Chirality : 0.044 0.183 5296 Planarity : 0.003 0.031 5640 Dihedral : 4.242 28.448 4456 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.13), residues: 4112 helix: 1.50 (0.12), residues: 1920 sheet: 0.74 (0.18), residues: 696 loop : -1.22 (0.14), residues: 1496 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 447 time to evaluate : 3.898 Fit side-chains revert: symmetry clash outliers start: 90 outliers final: 25 residues processed: 491 average time/residue: 1.1993 time to fit residues: 721.0013 Evaluate side-chains 432 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 407 time to evaluate : 3.777 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 19 residues processed: 10 average time/residue: 0.4050 time to fit residues: 11.8307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 373 optimal weight: 4.9990 chunk 284 optimal weight: 5.9990 chunk 196 optimal weight: 8.9990 chunk 41 optimal weight: 0.6980 chunk 180 optimal weight: 4.9990 chunk 254 optimal weight: 0.9990 chunk 379 optimal weight: 9.9990 chunk 402 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 359 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 ASN ** B 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 571 HIS ** D 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 GLN ** F 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 ASN ** G 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 467 ASN H 571 HIS ** H 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 32752 Z= 0.358 Angle : 0.669 9.081 44376 Z= 0.351 Chirality : 0.048 0.175 5296 Planarity : 0.005 0.042 5640 Dihedral : 4.809 28.667 4456 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 3.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.13), residues: 4112 helix: 1.20 (0.12), residues: 1920 sheet: 0.83 (0.18), residues: 712 loop : -1.23 (0.15), residues: 1480 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 422 time to evaluate : 3.639 Fit side-chains revert: symmetry clash outliers start: 120 outliers final: 40 residues processed: 494 average time/residue: 1.1695 time to fit residues: 708.0253 Evaluate side-chains 443 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 403 time to evaluate : 3.890 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 29 residues processed: 15 average time/residue: 0.3310 time to fit residues: 13.9609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 334 optimal weight: 0.7980 chunk 228 optimal weight: 0.7980 chunk 5 optimal weight: 0.0870 chunk 299 optimal weight: 6.9990 chunk 165 optimal weight: 7.9990 chunk 343 optimal weight: 3.9990 chunk 277 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 360 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 32752 Z= 0.179 Angle : 0.550 6.900 44376 Z= 0.284 Chirality : 0.044 0.175 5296 Planarity : 0.003 0.031 5640 Dihedral : 4.391 28.707 4456 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 2.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.13), residues: 4112 helix: 1.60 (0.12), residues: 1920 sheet: 0.98 (0.18), residues: 696 loop : -1.10 (0.15), residues: 1496 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 422 time to evaluate : 3.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 30 residues processed: 472 average time/residue: 1.2101 time to fit residues: 697.4816 Evaluate side-chains 432 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 402 time to evaluate : 3.642 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 26 residues processed: 10 average time/residue: 0.5207 time to fit residues: 12.6972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 135 optimal weight: 3.9990 chunk 362 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 chunk 236 optimal weight: 0.0010 chunk 99 optimal weight: 1.9990 chunk 402 optimal weight: 6.9990 chunk 334 optimal weight: 4.9990 chunk 186 optimal weight: 0.2980 chunk 33 optimal weight: 0.5980 chunk 133 optimal weight: 7.9990 chunk 211 optimal weight: 0.6980 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 32752 Z= 0.138 Angle : 0.513 8.565 44376 Z= 0.263 Chirality : 0.043 0.172 5296 Planarity : 0.003 0.031 5640 Dihedral : 4.027 28.101 4456 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.13), residues: 4112 helix: 1.90 (0.12), residues: 1928 sheet: 1.14 (0.18), residues: 696 loop : -1.12 (0.14), residues: 1488 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 428 time to evaluate : 4.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 31 residues processed: 474 average time/residue: 1.1660 time to fit residues: 681.5952 Evaluate side-chains 424 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 393 time to evaluate : 3.501 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 23 residues processed: 13 average time/residue: 0.3886 time to fit residues: 13.3951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 388 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 229 optimal weight: 4.9990 chunk 293 optimal weight: 2.9990 chunk 227 optimal weight: 0.7980 chunk 338 optimal weight: 0.8980 chunk 224 optimal weight: 6.9990 chunk 400 optimal weight: 5.9990 chunk 250 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 185 optimal weight: 0.0970 overall best weight: 1.0580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 467 ASN E 467 ASN F 467 ASN H 467 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 32752 Z= 0.192 Angle : 0.557 9.085 44376 Z= 0.287 Chirality : 0.044 0.168 5296 Planarity : 0.003 0.031 5640 Dihedral : 4.216 27.753 4456 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.13), residues: 4112 helix: 1.82 (0.12), residues: 1936 sheet: 1.14 (0.18), residues: 712 loop : -1.20 (0.14), residues: 1464 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 399 time to evaluate : 3.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 34 residues processed: 442 average time/residue: 1.2546 time to fit residues: 687.0509 Evaluate side-chains 430 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 396 time to evaluate : 3.622 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 28 residues processed: 12 average time/residue: 0.3177 time to fit residues: 12.0734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 248 optimal weight: 4.9990 chunk 160 optimal weight: 9.9990 chunk 239 optimal weight: 3.9990 chunk 120 optimal weight: 0.0070 chunk 78 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 254 optimal weight: 1.9990 chunk 273 optimal weight: 8.9990 chunk 198 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 315 optimal weight: 1.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 467 ASN E 467 ASN F 467 ASN H 467 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 32752 Z= 0.164 Angle : 0.538 8.311 44376 Z= 0.277 Chirality : 0.043 0.169 5296 Planarity : 0.003 0.031 5640 Dihedral : 4.095 27.717 4456 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.13), residues: 4112 helix: 1.87 (0.12), residues: 1936 sheet: 1.28 (0.18), residues: 696 loop : -1.07 (0.14), residues: 1480 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 404 time to evaluate : 3.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 36 residues processed: 442 average time/residue: 1.1553 time to fit residues: 634.3337 Evaluate side-chains 419 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 383 time to evaluate : 3.773 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 28 residues processed: 14 average time/residue: 0.3917 time to fit residues: 14.3984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 364 optimal weight: 5.9990 chunk 384 optimal weight: 0.9980 chunk 350 optimal weight: 0.9980 chunk 373 optimal weight: 6.9990 chunk 224 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 293 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 337 optimal weight: 1.9990 chunk 353 optimal weight: 0.8980 chunk 372 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 467 ASN E 467 ASN F 467 ASN H 467 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 32752 Z= 0.186 Angle : 0.556 8.452 44376 Z= 0.286 Chirality : 0.044 0.171 5296 Planarity : 0.003 0.030 5640 Dihedral : 4.173 27.414 4456 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.13), residues: 4112 helix: 1.85 (0.12), residues: 1928 sheet: 1.19 (0.18), residues: 712 loop : -1.09 (0.14), residues: 1472 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 392 time to evaluate : 4.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 32 residues processed: 432 average time/residue: 1.1877 time to fit residues: 644.2888 Evaluate side-chains 413 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 381 time to evaluate : 3.708 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 30 residues processed: 8 average time/residue: 0.3677 time to fit residues: 10.4870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 245 optimal weight: 0.3980 chunk 395 optimal weight: 0.9980 chunk 241 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 274 optimal weight: 20.0000 chunk 414 optimal weight: 3.9990 chunk 381 optimal weight: 0.8980 chunk 330 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 254 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 467 ASN E 467 ASN F 467 ASN H 467 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 32752 Z= 0.195 Angle : 0.564 8.447 44376 Z= 0.290 Chirality : 0.044 0.169 5296 Planarity : 0.003 0.030 5640 Dihedral : 4.187 27.317 4456 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.13), residues: 4112 helix: 1.79 (0.12), residues: 1936 sheet: 1.18 (0.17), residues: 712 loop : -1.12 (0.14), residues: 1464 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 393 time to evaluate : 4.011 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 35 residues processed: 421 average time/residue: 1.1437 time to fit residues: 598.6776 Evaluate side-chains 416 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 381 time to evaluate : 4.297 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 31 residues processed: 11 average time/residue: 0.3790 time to fit residues: 12.2629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 262 optimal weight: 1.9990 chunk 351 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 304 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 330 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 339 optimal weight: 3.9990 chunk 41 optimal weight: 0.0670 chunk 60 optimal weight: 0.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 467 ASN E 467 ASN F 467 ASN H 467 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.196578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.167823 restraints weight = 29333.020| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 0.84 r_work: 0.3819 rms_B_bonded: 0.94 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work: 0.3602 rms_B_bonded: 4.02 restraints_weight: 0.1250 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 32752 Z= 0.168 Angle : 0.545 8.017 44376 Z= 0.280 Chirality : 0.043 0.167 5296 Planarity : 0.003 0.031 5640 Dihedral : 4.060 27.449 4456 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.13), residues: 4112 helix: 1.86 (0.12), residues: 1936 sheet: 1.30 (0.18), residues: 696 loop : -1.02 (0.15), residues: 1480 =============================================================================== Job complete usr+sys time: 10256.73 seconds wall clock time: 184 minutes 4.57 seconds (11044.57 seconds total)