Starting phenix.real_space_refine on Fri Dec 8 19:15:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvu_41651/12_2023/8tvu_41651.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvu_41651/12_2023/8tvu_41651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvu_41651/12_2023/8tvu_41651.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvu_41651/12_2023/8tvu_41651.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvu_41651/12_2023/8tvu_41651.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvu_41651/12_2023/8tvu_41651.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 39348 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 324 5.16 5 C 45828 2.51 5 N 12516 2.21 5 O 14172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 306": "OE1" <-> "OE2" Residue "B TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 595": "OE1" <-> "OE2" Residue "B GLU 621": "OE1" <-> "OE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C GLU 112": "OE1" <-> "OE2" Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 396": "OE1" <-> "OE2" Residue "D GLU 595": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E ASP 62": "OD1" <-> "OD2" Residue "E GLU 69": "OE1" <-> "OE2" Residue "F GLU 296": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 112": "OE1" <-> "OE2" Residue "H GLU 133": "OE1" <-> "OE2" Residue "H PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 221": "OE1" <-> "OE2" Residue "H GLU 314": "OE1" <-> "OE2" Residue "H GLU 595": "OE1" <-> "OE2" Residue "H GLU 621": "OE1" <-> "OE2" Residue "I GLU 41": "OE1" <-> "OE2" Residue "I GLU 69": "OE1" <-> "OE2" Residue "J GLU 189": "OE1" <-> "OE2" Residue "J GLU 396": "OE1" <-> "OE2" Residue "L ARG 171": "NH1" <-> "NH2" Residue "L GLU 296": "OE1" <-> "OE2" Residue "L GLU 306": "OE1" <-> "OE2" Residue "L GLU 621": "OE1" <-> "OE2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "M GLU 69": "OE1" <-> "OE2" Residue "N GLU 70": "OE1" <-> "OE2" Residue "N PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 595": "OE1" <-> "OE2" Residue "O GLU 41": "OE1" <-> "OE2" Residue "O GLU 69": "OE1" <-> "OE2" Residue "O GLU 112": "OE1" <-> "OE2" Residue "P GLU 354": "OE1" <-> "OE2" Residue "P GLU 414": "OE1" <-> "OE2" Residue "P GLU 515": "OE1" <-> "OE2" Residue "Q GLU 69": "OE1" <-> "OE2" Residue "Q GLU 112": "OE1" <-> "OE2" Residue "R GLU 221": "OE1" <-> "OE2" Residue "R GLU 595": "OE1" <-> "OE2" Residue "R GLU 621": "OE1" <-> "OE2" Residue "T GLU 70": "OE1" <-> "OE2" Residue "T PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 306": "OE1" <-> "OE2" Residue "V GLU 69": "OE1" <-> "OE2" Residue "V GLU 112": "OE1" <-> "OE2" Residue "W GLU 414": "OE1" <-> "OE2" Residue "X GLU 41": "OE1" <-> "OE2" Residue "X GLU 112": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 72840 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4904 Classifications: {'peptide': 608} Link IDs: {'PTRANS': 28, 'TRANS': 579} Chain breaks: 2 Chain: "a" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1166 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "B" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4904 Classifications: {'peptide': 608} Link IDs: {'PTRANS': 28, 'TRANS': 579} Chain breaks: 2 Chain: "C" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1166 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "D" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4904 Classifications: {'peptide': 608} Link IDs: {'PTRANS': 28, 'TRANS': 579} Chain breaks: 2 Chain: "E" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1166 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "F" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4904 Classifications: {'peptide': 608} Link IDs: {'PTRANS': 28, 'TRANS': 579} Chain breaks: 2 Chain: "G" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1166 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "H" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4904 Classifications: {'peptide': 608} Link IDs: {'PTRANS': 28, 'TRANS': 579} Chain breaks: 2 Chain: "I" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1166 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "J" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4904 Classifications: {'peptide': 608} Link IDs: {'PTRANS': 28, 'TRANS': 579} Chain breaks: 2 Chain: "K" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1166 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "L" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4904 Classifications: {'peptide': 608} Link IDs: {'PTRANS': 28, 'TRANS': 579} Chain breaks: 2 Chain: "M" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1166 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "N" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4904 Classifications: {'peptide': 608} Link IDs: {'PTRANS': 28, 'TRANS': 579} Chain breaks: 2 Chain: "O" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1166 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "P" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4904 Classifications: {'peptide': 608} Link IDs: {'PTRANS': 28, 'TRANS': 579} Chain breaks: 2 Chain: "Q" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1166 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "R" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4904 Classifications: {'peptide': 608} Link IDs: {'PTRANS': 28, 'TRANS': 579} Chain breaks: 2 Chain: "S" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1166 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "T" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4904 Classifications: {'peptide': 608} Link IDs: {'PTRANS': 28, 'TRANS': 579} Chain breaks: 2 Chain: "V" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1166 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "W" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4904 Classifications: {'peptide': 608} Link IDs: {'PTRANS': 28, 'TRANS': 579} Chain breaks: 2 Chain: "X" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1166 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Time building chain proxies: 26.78, per 1000 atoms: 0.37 Number of scatterers: 72840 At special positions: 0 Unit cell: (185.365, 185.365, 237.827, 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 324 16.00 O 14172 8.00 N 12516 7.00 C 45828 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: 20.28 Conformation dependent library (CDL) restraints added in 9.9 seconds 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17280 Finding SS restraints... Secondary structure from input PDB file: 298 helices and 108 sheets defined 48.3% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.25 Creating SS restraints... Processing helix chain 'A' and resid 6 through 22 Processing helix chain 'A' and resid 22 through 38 Processing helix chain 'A' and resid 60 through 73 Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 104 through 121 removed outlier: 3.711A pdb=" N LYS A 108 " --> pdb=" O HIS A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 180 through 191 Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.574A pdb=" N ASP A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 322 No H-bonds generated for 'chain 'A' and resid 320 through 322' Processing helix chain 'A' and resid 323 through 343 removed outlier: 3.538A pdb=" N ALA A 338 " --> pdb=" O MET A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 398 through 416 Processing helix chain 'A' and resid 446 through 472 Processing helix chain 'A' and resid 526 through 540 Processing helix chain 'A' and resid 545 through 558 removed outlier: 3.656A pdb=" N TYR A 549 " --> pdb=" O GLY A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 579 Processing helix chain 'A' and resid 586 through 602 Processing helix chain 'A' and resid 605 through 647 Processing helix chain 'a' and resid 5 through 17 Processing helix chain 'a' and resid 29 through 48 Processing helix chain 'a' and resid 76 through 78 No H-bonds generated for 'chain 'a' and resid 76 through 78' Processing helix chain 'a' and resid 79 through 92 Processing helix chain 'a' and resid 93 through 96 Processing helix chain 'a' and resid 100 through 122 removed outlier: 4.440A pdb=" N GLN a 117 " --> pdb=" O LEU a 113 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N THR a 118 " --> pdb=" O LEU a 114 " (cutoff:3.500A) Processing helix chain 'a' and resid 138 through 144 Processing helix chain 'B' and resid 6 through 22 Processing helix chain 'B' and resid 22 through 38 Processing helix chain 'B' and resid 60 through 73 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 104 through 121 removed outlier: 3.743A pdb=" N LYS B 108 " --> pdb=" O HIS B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 180 through 192 Processing helix chain 'B' and resid 256 through 262 removed outlier: 3.570A pdb=" N ASP B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 322 No H-bonds generated for 'chain 'B' and resid 320 through 322' Processing helix chain 'B' and resid 323 through 343 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 398 through 416 Processing helix chain 'B' and resid 446 through 472 Processing helix chain 'B' and resid 526 through 540 Processing helix chain 'B' and resid 545 through 558 removed outlier: 3.658A pdb=" N TYR B 549 " --> pdb=" O GLY B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 579 Processing helix chain 'B' and resid 586 through 602 Processing helix chain 'B' and resid 605 through 647 Processing helix chain 'C' and resid 5 through 17 Processing helix chain 'C' and resid 29 through 48 Processing helix chain 'C' and resid 79 through 92 Processing helix chain 'C' and resid 93 through 96 Processing helix chain 'C' and resid 100 through 122 removed outlier: 4.450A pdb=" N GLN C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 144 Processing helix chain 'D' and resid 6 through 22 Processing helix chain 'D' and resid 22 through 38 Processing helix chain 'D' and resid 60 through 73 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 104 through 121 removed outlier: 3.756A pdb=" N LYS D 108 " --> pdb=" O HIS D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 180 through 191 Processing helix chain 'D' and resid 256 through 262 removed outlier: 3.547A pdb=" N ASP D 260 " --> pdb=" O ASP D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 322 No H-bonds generated for 'chain 'D' and resid 320 through 322' Processing helix chain 'D' and resid 323 through 343 Processing helix chain 'D' and resid 359 through 363 removed outlier: 3.511A pdb=" N TYR D 363 " --> pdb=" O GLU D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 416 Processing helix chain 'D' and resid 446 through 472 Processing helix chain 'D' and resid 526 through 540 Processing helix chain 'D' and resid 545 through 558 removed outlier: 3.630A pdb=" N TYR D 549 " --> pdb=" O GLY D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 579 removed outlier: 3.501A pdb=" N MET D 579 " --> pdb=" O GLN D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 602 Processing helix chain 'D' and resid 605 through 647 Processing helix chain 'E' and resid 5 through 17 Processing helix chain 'E' and resid 29 through 48 Processing helix chain 'E' and resid 79 through 92 Processing helix chain 'E' and resid 93 through 96 Processing helix chain 'E' and resid 100 through 122 removed outlier: 4.437A pdb=" N GLN E 117 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N THR E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 144 Processing helix chain 'F' and resid 6 through 22 Processing helix chain 'F' and resid 22 through 38 Processing helix chain 'F' and resid 59 through 73 removed outlier: 4.323A pdb=" N VAL F 63 " --> pdb=" O VAL F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 102 Processing helix chain 'F' and resid 104 through 121 removed outlier: 3.711A pdb=" N LYS F 108 " --> pdb=" O HIS F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 155 Processing helix chain 'F' and resid 180 through 192 Processing helix chain 'F' and resid 256 through 262 removed outlier: 3.571A pdb=" N ASP F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 322 No H-bonds generated for 'chain 'F' and resid 320 through 322' Processing helix chain 'F' and resid 323 through 343 Processing helix chain 'F' and resid 359 through 363 Processing helix chain 'F' and resid 398 through 416 Processing helix chain 'F' and resid 446 through 472 Processing helix chain 'F' and resid 526 through 540 Processing helix chain 'F' and resid 545 through 558 removed outlier: 3.665A pdb=" N TYR F 549 " --> pdb=" O GLY F 545 " (cutoff:3.500A) Processing helix chain 'F' and resid 563 through 579 Processing helix chain 'F' and resid 586 through 602 Processing helix chain 'F' and resid 605 through 647 Processing helix chain 'G' and resid 5 through 17 Processing helix chain 'G' and resid 29 through 48 Processing helix chain 'G' and resid 76 through 78 No H-bonds generated for 'chain 'G' and resid 76 through 78' Processing helix chain 'G' and resid 79 through 92 Processing helix chain 'G' and resid 93 through 96 Processing helix chain 'G' and resid 100 through 122 removed outlier: 4.435A pdb=" N GLN G 117 " --> pdb=" O LEU G 113 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR G 118 " --> pdb=" O LEU G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 144 Processing helix chain 'H' and resid 6 through 22 Processing helix chain 'H' and resid 22 through 38 Processing helix chain 'H' and resid 60 through 73 Processing helix chain 'H' and resid 91 through 102 Processing helix chain 'H' and resid 104 through 121 removed outlier: 3.749A pdb=" N LYS H 108 " --> pdb=" O HIS H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 155 Processing helix chain 'H' and resid 180 through 192 Processing helix chain 'H' and resid 256 through 262 removed outlier: 3.558A pdb=" N ASP H 260 " --> pdb=" O ASP H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 320 through 322 No H-bonds generated for 'chain 'H' and resid 320 through 322' Processing helix chain 'H' and resid 323 through 343 Processing helix chain 'H' and resid 359 through 363 Processing helix chain 'H' and resid 398 through 416 Processing helix chain 'H' and resid 446 through 472 Processing helix chain 'H' and resid 526 through 540 Processing helix chain 'H' and resid 545 through 558 removed outlier: 3.661A pdb=" N TYR H 549 " --> pdb=" O GLY H 545 " (cutoff:3.500A) Processing helix chain 'H' and resid 563 through 579 Processing helix chain 'H' and resid 586 through 602 Processing helix chain 'H' and resid 605 through 647 Processing helix chain 'I' and resid 5 through 17 Processing helix chain 'I' and resid 29 through 48 Processing helix chain 'I' and resid 76 through 78 No H-bonds generated for 'chain 'I' and resid 76 through 78' Processing helix chain 'I' and resid 79 through 92 Processing helix chain 'I' and resid 93 through 96 Processing helix chain 'I' and resid 100 through 122 removed outlier: 4.451A pdb=" N GLN I 117 " --> pdb=" O LEU I 113 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR I 118 " --> pdb=" O LEU I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 144 Processing helix chain 'J' and resid 6 through 22 Processing helix chain 'J' and resid 22 through 38 Processing helix chain 'J' and resid 60 through 73 Processing helix chain 'J' and resid 91 through 102 Processing helix chain 'J' and resid 104 through 121 removed outlier: 3.782A pdb=" N LYS J 108 " --> pdb=" O HIS J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 155 Processing helix chain 'J' and resid 180 through 191 Processing helix chain 'J' and resid 256 through 262 removed outlier: 3.537A pdb=" N ASP J 260 " --> pdb=" O ASP J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 320 through 322 No H-bonds generated for 'chain 'J' and resid 320 through 322' Processing helix chain 'J' and resid 323 through 343 Processing helix chain 'J' and resid 359 through 363 removed outlier: 3.514A pdb=" N TYR J 363 " --> pdb=" O GLU J 360 " (cutoff:3.500A) Processing helix chain 'J' and resid 398 through 416 Processing helix chain 'J' and resid 446 through 472 Processing helix chain 'J' and resid 526 through 540 Processing helix chain 'J' and resid 545 through 558 removed outlier: 3.647A pdb=" N TYR J 549 " --> pdb=" O GLY J 545 " (cutoff:3.500A) Processing helix chain 'J' and resid 563 through 579 Processing helix chain 'J' and resid 586 through 602 Processing helix chain 'J' and resid 605 through 647 Processing helix chain 'K' and resid 5 through 17 Processing helix chain 'K' and resid 29 through 48 Processing helix chain 'K' and resid 76 through 78 No H-bonds generated for 'chain 'K' and resid 76 through 78' Processing helix chain 'K' and resid 79 through 92 Processing helix chain 'K' and resid 93 through 96 Processing helix chain 'K' and resid 100 through 122 removed outlier: 4.439A pdb=" N GLN K 117 " --> pdb=" O LEU K 113 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N THR K 118 " --> pdb=" O LEU K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 144 Processing helix chain 'L' and resid 6 through 22 Processing helix chain 'L' and resid 22 through 38 Processing helix chain 'L' and resid 60 through 73 Processing helix chain 'L' and resid 91 through 102 Processing helix chain 'L' and resid 104 through 121 removed outlier: 3.794A pdb=" N LYS L 108 " --> pdb=" O HIS L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 155 Processing helix chain 'L' and resid 180 through 191 Processing helix chain 'L' and resid 256 through 262 removed outlier: 3.541A pdb=" N ASP L 260 " --> pdb=" O ASP L 256 " (cutoff:3.500A) Processing helix chain 'L' and resid 320 through 322 No H-bonds generated for 'chain 'L' and resid 320 through 322' Processing helix chain 'L' and resid 323 through 343 Processing helix chain 'L' and resid 359 through 363 removed outlier: 3.513A pdb=" N TYR L 363 " --> pdb=" O GLU L 360 " (cutoff:3.500A) Processing helix chain 'L' and resid 398 through 416 Processing helix chain 'L' and resid 446 through 472 Processing helix chain 'L' and resid 526 through 540 Processing helix chain 'L' and resid 545 through 558 removed outlier: 3.645A pdb=" N TYR L 549 " --> pdb=" O GLY L 545 " (cutoff:3.500A) Processing helix chain 'L' and resid 563 through 579 Processing helix chain 'L' and resid 586 through 602 Processing helix chain 'L' and resid 605 through 647 Processing helix chain 'M' and resid 5 through 17 Processing helix chain 'M' and resid 29 through 48 Processing helix chain 'M' and resid 76 through 78 No H-bonds generated for 'chain 'M' and resid 76 through 78' Processing helix chain 'M' and resid 79 through 92 Processing helix chain 'M' and resid 93 through 96 Processing helix chain 'M' and resid 100 through 122 removed outlier: 4.443A pdb=" N GLN M 117 " --> pdb=" O LEU M 113 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N THR M 118 " --> pdb=" O LEU M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 138 through 144 Processing helix chain 'N' and resid 6 through 22 Processing helix chain 'N' and resid 22 through 38 Processing helix chain 'N' and resid 60 through 73 Processing helix chain 'N' and resid 91 through 102 Processing helix chain 'N' and resid 104 through 121 removed outlier: 3.753A pdb=" N LYS N 108 " --> pdb=" O HIS N 104 " (cutoff:3.500A) Processing helix chain 'N' and resid 151 through 155 Processing helix chain 'N' and resid 180 through 192 Processing helix chain 'N' and resid 256 through 262 removed outlier: 3.613A pdb=" N ASP N 260 " --> pdb=" O ASP N 256 " (cutoff:3.500A) Processing helix chain 'N' and resid 320 through 322 No H-bonds generated for 'chain 'N' and resid 320 through 322' Processing helix chain 'N' and resid 323 through 343 Processing helix chain 'N' and resid 359 through 363 Processing helix chain 'N' and resid 398 through 416 Processing helix chain 'N' and resid 446 through 472 Processing helix chain 'N' and resid 526 through 540 Processing helix chain 'N' and resid 545 through 558 removed outlier: 3.662A pdb=" N TYR N 549 " --> pdb=" O GLY N 545 " (cutoff:3.500A) Processing helix chain 'N' and resid 563 through 579 Processing helix chain 'N' and resid 586 through 602 Processing helix chain 'N' and resid 605 through 647 Processing helix chain 'O' and resid 5 through 17 Processing helix chain 'O' and resid 29 through 48 Processing helix chain 'O' and resid 79 through 92 Processing helix chain 'O' and resid 93 through 96 Processing helix chain 'O' and resid 100 through 122 removed outlier: 4.447A pdb=" N GLN O 117 " --> pdb=" O LEU O 113 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N THR O 118 " --> pdb=" O LEU O 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 138 through 144 Processing helix chain 'P' and resid 6 through 22 Processing helix chain 'P' and resid 22 through 38 Processing helix chain 'P' and resid 60 through 73 Processing helix chain 'P' and resid 91 through 102 Processing helix chain 'P' and resid 104 through 121 removed outlier: 3.792A pdb=" N LYS P 108 " --> pdb=" O HIS P 104 " (cutoff:3.500A) Processing helix chain 'P' and resid 151 through 155 Processing helix chain 'P' and resid 180 through 191 Processing helix chain 'P' and resid 256 through 262 removed outlier: 3.549A pdb=" N ASP P 260 " --> pdb=" O ASP P 256 " (cutoff:3.500A) Processing helix chain 'P' and resid 320 through 322 No H-bonds generated for 'chain 'P' and resid 320 through 322' Processing helix chain 'P' and resid 323 through 343 Processing helix chain 'P' and resid 359 through 363 removed outlier: 3.507A pdb=" N TYR P 363 " --> pdb=" O GLU P 360 " (cutoff:3.500A) Processing helix chain 'P' and resid 398 through 416 Processing helix chain 'P' and resid 446 through 472 Processing helix chain 'P' and resid 526 through 540 Processing helix chain 'P' and resid 545 through 558 removed outlier: 3.618A pdb=" N TYR P 549 " --> pdb=" O GLY P 545 " (cutoff:3.500A) Processing helix chain 'P' and resid 563 through 579 Processing helix chain 'P' and resid 586 through 602 Processing helix chain 'P' and resid 605 through 647 Processing helix chain 'Q' and resid 5 through 17 Processing helix chain 'Q' and resid 29 through 48 Processing helix chain 'Q' and resid 76 through 78 No H-bonds generated for 'chain 'Q' and resid 76 through 78' Processing helix chain 'Q' and resid 79 through 92 Processing helix chain 'Q' and resid 93 through 96 Processing helix chain 'Q' and resid 100 through 122 removed outlier: 4.442A pdb=" N GLN Q 117 " --> pdb=" O LEU Q 113 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N THR Q 118 " --> pdb=" O LEU Q 114 " (cutoff:3.500A) Processing helix chain 'Q' and resid 138 through 144 Processing helix chain 'R' and resid 6 through 22 Processing helix chain 'R' and resid 22 through 38 Processing helix chain 'R' and resid 60 through 73 Processing helix chain 'R' and resid 91 through 102 Processing helix chain 'R' and resid 104 through 121 removed outlier: 3.710A pdb=" N LYS R 108 " --> pdb=" O HIS R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 155 Processing helix chain 'R' and resid 180 through 192 Processing helix chain 'R' and resid 256 through 262 removed outlier: 3.555A pdb=" N ASP R 260 " --> pdb=" O ASP R 256 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 322 No H-bonds generated for 'chain 'R' and resid 320 through 322' Processing helix chain 'R' and resid 323 through 343 removed outlier: 3.528A pdb=" N ALA R 338 " --> pdb=" O MET R 334 " (cutoff:3.500A) Processing helix chain 'R' and resid 359 through 363 Processing helix chain 'R' and resid 398 through 416 Processing helix chain 'R' and resid 446 through 472 Processing helix chain 'R' and resid 526 through 540 Processing helix chain 'R' and resid 545 through 558 removed outlier: 3.690A pdb=" N TYR R 549 " --> pdb=" O GLY R 545 " (cutoff:3.500A) Processing helix chain 'R' and resid 563 through 579 Processing helix chain 'R' and resid 586 through 602 Processing helix chain 'R' and resid 605 through 647 Processing helix chain 'S' and resid 5 through 17 Processing helix chain 'S' and resid 29 through 48 Processing helix chain 'S' and resid 76 through 78 No H-bonds generated for 'chain 'S' and resid 76 through 78' Processing helix chain 'S' and resid 79 through 92 Processing helix chain 'S' and resid 93 through 96 Processing helix chain 'S' and resid 100 through 122 removed outlier: 4.432A pdb=" N GLN S 117 " --> pdb=" O LEU S 113 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N THR S 118 " --> pdb=" O LEU S 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 138 through 144 Processing helix chain 'T' and resid 6 through 22 Processing helix chain 'T' and resid 22 through 38 Processing helix chain 'T' and resid 60 through 73 Processing helix chain 'T' and resid 91 through 102 Processing helix chain 'T' and resid 104 through 121 removed outlier: 3.747A pdb=" N LYS T 108 " --> pdb=" O HIS T 104 " (cutoff:3.500A) Processing helix chain 'T' and resid 151 through 155 Processing helix chain 'T' and resid 180 through 192 Processing helix chain 'T' and resid 256 through 262 removed outlier: 3.602A pdb=" N ASP T 260 " --> pdb=" O ASP T 256 " (cutoff:3.500A) Processing helix chain 'T' and resid 320 through 322 No H-bonds generated for 'chain 'T' and resid 320 through 322' Processing helix chain 'T' and resid 323 through 343 Processing helix chain 'T' and resid 359 through 363 Processing helix chain 'T' and resid 398 through 416 Processing helix chain 'T' and resid 446 through 472 Processing helix chain 'T' and resid 526 through 540 Processing helix chain 'T' and resid 545 through 558 removed outlier: 3.668A pdb=" N TYR T 549 " --> pdb=" O GLY T 545 " (cutoff:3.500A) Processing helix chain 'T' and resid 563 through 579 Processing helix chain 'T' and resid 586 through 602 Processing helix chain 'T' and resid 605 through 647 Processing helix chain 'V' and resid 5 through 17 Processing helix chain 'V' and resid 29 through 48 Processing helix chain 'V' and resid 76 through 78 No H-bonds generated for 'chain 'V' and resid 76 through 78' Processing helix chain 'V' and resid 79 through 92 removed outlier: 3.509A pdb=" N VAL V 83 " --> pdb=" O ALA V 79 " (cutoff:3.500A) Processing helix chain 'V' and resid 93 through 96 Processing helix chain 'V' and resid 100 through 122 removed outlier: 4.452A pdb=" N GLN V 117 " --> pdb=" O LEU V 113 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR V 118 " --> pdb=" O LEU V 114 " (cutoff:3.500A) Processing helix chain 'V' and resid 138 through 144 Processing helix chain 'W' and resid 6 through 22 Processing helix chain 'W' and resid 22 through 38 Processing helix chain 'W' and resid 59 through 73 removed outlier: 4.388A pdb=" N VAL W 63 " --> pdb=" O VAL W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 91 through 102 Processing helix chain 'W' and resid 104 through 121 removed outlier: 3.708A pdb=" N LYS W 108 " --> pdb=" O HIS W 104 " (cutoff:3.500A) Processing helix chain 'W' and resid 151 through 155 Processing helix chain 'W' and resid 180 through 192 Processing helix chain 'W' and resid 248 through 251 removed outlier: 3.835A pdb=" N ILE W 251 " --> pdb=" O LYS W 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 248 through 251' Processing helix chain 'W' and resid 256 through 262 removed outlier: 3.557A pdb=" N ASP W 260 " --> pdb=" O ASP W 256 " (cutoff:3.500A) Processing helix chain 'W' and resid 320 through 322 No H-bonds generated for 'chain 'W' and resid 320 through 322' Processing helix chain 'W' and resid 323 through 343 Processing helix chain 'W' and resid 359 through 363 Processing helix chain 'W' and resid 398 through 416 Processing helix chain 'W' and resid 446 through 472 Processing helix chain 'W' and resid 526 through 540 Processing helix chain 'W' and resid 545 through 558 removed outlier: 3.675A pdb=" N TYR W 549 " --> pdb=" O GLY W 545 " (cutoff:3.500A) Processing helix chain 'W' and resid 563 through 579 Processing helix chain 'W' and resid 586 through 602 Processing helix chain 'W' and resid 605 through 647 Processing helix chain 'X' and resid 5 through 17 Processing helix chain 'X' and resid 29 through 48 Processing helix chain 'X' and resid 76 through 78 No H-bonds generated for 'chain 'X' and resid 76 through 78' Processing helix chain 'X' and resid 79 through 92 Processing helix chain 'X' and resid 93 through 96 Processing helix chain 'X' and resid 100 through 122 removed outlier: 4.437A pdb=" N GLN X 117 " --> pdb=" O LEU X 113 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N THR X 118 " --> pdb=" O LEU X 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 138 through 144 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 82 Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 149 removed outlier: 3.707A pdb=" N ILE A 149 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA A 125 " --> pdb=" O ILE A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 158 Processing sheet with id=AA4, first strand: chain 'A' and resid 156 through 158 removed outlier: 6.649A pdb=" N ALA A 220 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE A 280 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N PHE A 222 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS A 278 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLU A 224 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL A 276 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL A 226 " --> pdb=" O ARG A 274 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ARG A 274 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS A 228 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS A 272 " --> pdb=" O LYS A 228 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLU A 230 " --> pdb=" O GLN A 270 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLN A 270 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA A 232 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLU A 268 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE A 234 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE A 264 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL A 276 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ILE A 280 " --> pdb=" O ASP A 289 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ASP A 289 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 306 through 309 Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA7, first strand: chain 'A' and resid 372 through 373 removed outlier: 6.124A pdb=" N TYR A 372 " --> pdb=" O PHE B 351 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA B 390 " --> pdb=" O PHE B 350 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 377 through 378 Processing sheet with id=AA9, first strand: chain 'A' and resid 476 through 477 removed outlier: 3.620A pdb=" N ARG A 476 " --> pdb=" O ALA A 494 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 497 through 499 removed outlier: 3.768A pdb=" N ASP A 498 " --> pdb=" O VAL A 506 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 77 through 82 Processing sheet with id=AB3, first strand: chain 'B' and resid 142 through 149 removed outlier: 3.685A pdb=" N ILE B 149 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA B 125 " --> pdb=" O ILE B 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AB5, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.113A pdb=" N GLN B 236 " --> pdb=" O LYS B 265 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS B 265 " --> pdb=" O GLN B 236 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL B 276 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ILE B 280 " --> pdb=" O ASP B 289 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ASP B 289 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 306 through 309 Processing sheet with id=AB7, first strand: chain 'B' and resid 372 through 373 removed outlier: 6.137A pdb=" N TYR B 372 " --> pdb=" O PHE D 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 377 through 378 Processing sheet with id=AB9, first strand: chain 'B' and resid 476 through 477 removed outlier: 3.659A pdb=" N ARG B 476 " --> pdb=" O ALA B 494 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 497 through 499 removed outlier: 3.771A pdb=" N ASP B 498 " --> pdb=" O VAL B 506 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 77 through 82 Processing sheet with id=AC3, first strand: chain 'D' and resid 142 through 149 removed outlier: 3.626A pdb=" N ILE D 149 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ALA D 125 " --> pdb=" O ILE D 149 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 156 through 158 Processing sheet with id=AC5, first strand: chain 'D' and resid 156 through 158 removed outlier: 6.641A pdb=" N ALA D 220 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE D 280 " --> pdb=" O ALA D 220 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N PHE D 222 " --> pdb=" O LYS D 278 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS D 278 " --> pdb=" O PHE D 222 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLU D 224 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL D 276 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL D 226 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ARG D 274 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS D 228 " --> pdb=" O LYS D 272 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LYS D 272 " --> pdb=" O LYS D 228 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLU D 230 " --> pdb=" O GLN D 270 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLN D 270 " --> pdb=" O GLU D 230 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA D 232 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU D 268 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE D 234 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE D 264 " --> pdb=" O GLN D 236 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL D 276 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ILE D 280 " --> pdb=" O ASP D 289 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP D 289 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 306 through 309 Processing sheet with id=AC7, first strand: chain 'D' and resid 372 through 373 removed outlier: 6.100A pdb=" N TYR D 372 " --> pdb=" O PHE F 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 377 through 378 Processing sheet with id=AC9, first strand: chain 'D' and resid 476 through 477 removed outlier: 3.784A pdb=" N ARG D 476 " --> pdb=" O ALA D 494 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 497 through 499 removed outlier: 3.805A pdb=" N ASP D 498 " --> pdb=" O VAL D 506 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 77 through 82 Processing sheet with id=AD3, first strand: chain 'F' and resid 142 through 149 removed outlier: 3.706A pdb=" N ILE F 149 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA F 125 " --> pdb=" O ILE F 149 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 156 through 158 Processing sheet with id=AD5, first strand: chain 'F' and resid 156 through 158 removed outlier: 6.658A pdb=" N ALA F 220 " --> pdb=" O ILE F 280 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE F 280 " --> pdb=" O ALA F 220 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE F 222 " --> pdb=" O LYS F 278 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS F 278 " --> pdb=" O PHE F 222 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLU F 224 " --> pdb=" O VAL F 276 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL F 276 " --> pdb=" O GLU F 224 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL F 226 " --> pdb=" O ARG F 274 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ARG F 274 " --> pdb=" O VAL F 226 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LYS F 228 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LYS F 272 " --> pdb=" O LYS F 228 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLU F 230 " --> pdb=" O GLN F 270 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLN F 270 " --> pdb=" O GLU F 230 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA F 232 " --> pdb=" O GLU F 268 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU F 268 " --> pdb=" O ALA F 232 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE F 234 " --> pdb=" O ILE F 266 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE F 264 " --> pdb=" O GLN F 236 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL F 276 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE F 280 " --> pdb=" O ASP F 289 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ASP F 289 " --> pdb=" O ILE F 280 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 306 through 309 Processing sheet with id=AD7, first strand: chain 'F' and resid 372 through 373 removed outlier: 6.129A pdb=" N TYR F 372 " --> pdb=" O PHE H 351 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA H 390 " --> pdb=" O PHE H 350 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 377 through 378 Processing sheet with id=AD9, first strand: chain 'F' and resid 476 through 477 removed outlier: 3.598A pdb=" N ARG F 476 " --> pdb=" O ALA F 494 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 497 through 499 removed outlier: 3.761A pdb=" N ASP F 498 " --> pdb=" O VAL F 506 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 77 through 82 Processing sheet with id=AE3, first strand: chain 'H' and resid 142 through 149 removed outlier: 3.690A pdb=" N ILE H 149 " --> pdb=" O ALA H 125 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ALA H 125 " --> pdb=" O ILE H 149 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 156 through 158 Processing sheet with id=AE5, first strand: chain 'H' and resid 156 through 158 removed outlier: 6.174A pdb=" N GLN H 236 " --> pdb=" O LYS H 265 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LYS H 265 " --> pdb=" O GLN H 236 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL H 276 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ILE H 280 " --> pdb=" O ASP H 289 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASP H 289 " --> pdb=" O ILE H 280 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 306 through 309 Processing sheet with id=AE7, first strand: chain 'H' and resid 372 through 373 removed outlier: 6.126A pdb=" N TYR H 372 " --> pdb=" O PHE L 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'H' and resid 377 through 378 Processing sheet with id=AE9, first strand: chain 'H' and resid 476 through 477 removed outlier: 3.661A pdb=" N ARG H 476 " --> pdb=" O ALA H 494 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 497 through 499 removed outlier: 3.774A pdb=" N ASP H 498 " --> pdb=" O VAL H 506 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 77 through 82 Processing sheet with id=AF3, first strand: chain 'J' and resid 142 through 149 removed outlier: 3.626A pdb=" N ILE J 149 " --> pdb=" O ALA J 125 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ALA J 125 " --> pdb=" O ILE J 149 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 156 through 158 Processing sheet with id=AF5, first strand: chain 'J' and resid 156 through 158 removed outlier: 6.633A pdb=" N ALA J 220 " --> pdb=" O ILE J 280 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE J 280 " --> pdb=" O ALA J 220 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N PHE J 222 " --> pdb=" O LYS J 278 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS J 278 " --> pdb=" O PHE J 222 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU J 224 " --> pdb=" O VAL J 276 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL J 276 " --> pdb=" O GLU J 224 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL J 226 " --> pdb=" O ARG J 274 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ARG J 274 " --> pdb=" O VAL J 226 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS J 228 " --> pdb=" O LYS J 272 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS J 272 " --> pdb=" O LYS J 228 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLU J 230 " --> pdb=" O GLN J 270 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN J 270 " --> pdb=" O GLU J 230 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA J 232 " --> pdb=" O GLU J 268 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLU J 268 " --> pdb=" O ALA J 232 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE J 234 " --> pdb=" O ILE J 266 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE J 264 " --> pdb=" O GLN J 236 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL J 276 " --> pdb=" O ILE J 293 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ILE J 280 " --> pdb=" O ASP J 289 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ASP J 289 " --> pdb=" O ILE J 280 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 306 through 309 Processing sheet with id=AF7, first strand: chain 'J' and resid 390 through 391 removed outlier: 4.690A pdb=" N ALA J 390 " --> pdb=" O PHE J 350 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 377 through 378 Processing sheet with id=AF9, first strand: chain 'J' and resid 476 through 477 removed outlier: 3.739A pdb=" N ARG J 476 " --> pdb=" O ALA J 494 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 497 through 499 removed outlier: 3.777A pdb=" N ASP J 498 " --> pdb=" O VAL J 506 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 77 through 82 Processing sheet with id=AG3, first strand: chain 'L' and resid 142 through 149 removed outlier: 3.639A pdb=" N ILE L 149 " --> pdb=" O ALA L 125 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ALA L 125 " --> pdb=" O ILE L 149 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 156 through 158 Processing sheet with id=AG5, first strand: chain 'L' and resid 156 through 158 removed outlier: 6.636A pdb=" N ALA L 220 " --> pdb=" O ILE L 280 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE L 280 " --> pdb=" O ALA L 220 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE L 222 " --> pdb=" O LYS L 278 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS L 278 " --> pdb=" O PHE L 222 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLU L 224 " --> pdb=" O VAL L 276 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL L 276 " --> pdb=" O GLU L 224 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL L 226 " --> pdb=" O ARG L 274 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG L 274 " --> pdb=" O VAL L 226 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LYS L 228 " --> pdb=" O LYS L 272 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS L 272 " --> pdb=" O LYS L 228 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N GLU L 230 " --> pdb=" O GLN L 270 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLN L 270 " --> pdb=" O GLU L 230 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA L 232 " --> pdb=" O GLU L 268 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLU L 268 " --> pdb=" O ALA L 232 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE L 234 " --> pdb=" O ILE L 266 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE L 264 " --> pdb=" O GLN L 236 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL L 276 " --> pdb=" O ILE L 293 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE L 280 " --> pdb=" O ASP L 289 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ASP L 289 " --> pdb=" O ILE L 280 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 306 through 309 Processing sheet with id=AG7, first strand: chain 'L' and resid 372 through 373 removed outlier: 6.100A pdb=" N TYR L 372 " --> pdb=" O PHE W 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'L' and resid 377 through 378 Processing sheet with id=AG9, first strand: chain 'L' and resid 476 through 477 removed outlier: 3.749A pdb=" N ARG L 476 " --> pdb=" O ALA L 494 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 497 through 499 removed outlier: 3.771A pdb=" N ASP L 498 " --> pdb=" O VAL L 506 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 77 through 82 Processing sheet with id=AH3, first strand: chain 'N' and resid 142 through 149 removed outlier: 3.689A pdb=" N ILE N 149 " --> pdb=" O ALA N 125 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ALA N 125 " --> pdb=" O ILE N 149 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 156 through 158 Processing sheet with id=AH5, first strand: chain 'N' and resid 156 through 158 removed outlier: 6.118A pdb=" N GLN N 236 " --> pdb=" O LYS N 265 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS N 265 " --> pdb=" O GLN N 236 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL N 276 " --> pdb=" O ILE N 293 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ILE N 280 " --> pdb=" O ASP N 289 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ASP N 289 " --> pdb=" O ILE N 280 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'N' and resid 306 through 309 Processing sheet with id=AH7, first strand: chain 'N' and resid 390 through 391 removed outlier: 4.643A pdb=" N ALA N 390 " --> pdb=" O PHE N 350 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'N' and resid 377 through 378 Processing sheet with id=AH9, first strand: chain 'N' and resid 476 through 477 removed outlier: 3.666A pdb=" N ARG N 476 " --> pdb=" O ALA N 494 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'N' and resid 497 through 499 removed outlier: 3.900A pdb=" N ASP N 498 " --> pdb=" O VAL N 506 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'P' and resid 77 through 82 Processing sheet with id=AI3, first strand: chain 'P' and resid 142 through 149 removed outlier: 3.635A pdb=" N ILE P 149 " --> pdb=" O ALA P 125 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ALA P 125 " --> pdb=" O ILE P 149 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'P' and resid 156 through 158 Processing sheet with id=AI5, first strand: chain 'P' and resid 156 through 158 removed outlier: 6.663A pdb=" N ALA P 220 " --> pdb=" O ILE P 280 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE P 280 " --> pdb=" O ALA P 220 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE P 222 " --> pdb=" O LYS P 278 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS P 278 " --> pdb=" O PHE P 222 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU P 224 " --> pdb=" O VAL P 276 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL P 276 " --> pdb=" O GLU P 224 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL P 226 " --> pdb=" O ARG P 274 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG P 274 " --> pdb=" O VAL P 226 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LYS P 228 " --> pdb=" O LYS P 272 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS P 272 " --> pdb=" O LYS P 228 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLU P 230 " --> pdb=" O GLN P 270 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLN P 270 " --> pdb=" O GLU P 230 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA P 232 " --> pdb=" O GLU P 268 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU P 268 " --> pdb=" O ALA P 232 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE P 234 " --> pdb=" O ILE P 266 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE P 264 " --> pdb=" O GLN P 236 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL P 276 " --> pdb=" O ILE P 293 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ILE P 280 " --> pdb=" O ASP P 289 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ASP P 289 " --> pdb=" O ILE P 280 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'P' and resid 306 through 309 Processing sheet with id=AI7, first strand: chain 'P' and resid 390 through 391 removed outlier: 4.687A pdb=" N ALA P 390 " --> pdb=" O PHE P 350 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'P' and resid 372 through 373 removed outlier: 6.097A pdb=" N TYR P 372 " --> pdb=" O PHE R 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 Processing sheet with id=AI9, first strand: chain 'P' and resid 377 through 378 Processing sheet with id=AJ1, first strand: chain 'P' and resid 476 through 477 removed outlier: 3.738A pdb=" N ARG P 476 " --> pdb=" O ALA P 494 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'P' and resid 497 through 499 removed outlier: 3.782A pdb=" N ASP P 498 " --> pdb=" O VAL P 506 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'R' and resid 77 through 82 Processing sheet with id=AJ4, first strand: chain 'R' and resid 142 through 149 removed outlier: 3.707A pdb=" N ILE R 149 " --> pdb=" O ALA R 125 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA R 125 " --> pdb=" O ILE R 149 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'R' and resid 156 through 158 Processing sheet with id=AJ6, first strand: chain 'R' and resid 156 through 158 removed outlier: 6.677A pdb=" N ALA R 220 " --> pdb=" O ILE R 280 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE R 280 " --> pdb=" O ALA R 220 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N PHE R 222 " --> pdb=" O LYS R 278 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS R 278 " --> pdb=" O PHE R 222 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLU R 224 " --> pdb=" O VAL R 276 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL R 276 " --> pdb=" O GLU R 224 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL R 226 " --> pdb=" O ARG R 274 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ARG R 274 " --> pdb=" O VAL R 226 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS R 228 " --> pdb=" O LYS R 272 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYS R 272 " --> pdb=" O LYS R 228 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLU R 230 " --> pdb=" O GLN R 270 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLN R 270 " --> pdb=" O GLU R 230 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA R 232 " --> pdb=" O GLU R 268 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU R 268 " --> pdb=" O ALA R 232 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE R 234 " --> pdb=" O ILE R 266 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE R 264 " --> pdb=" O GLN R 236 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL R 276 " --> pdb=" O ILE R 293 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ILE R 280 " --> pdb=" O ASP R 289 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ASP R 289 " --> pdb=" O ILE R 280 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'R' and resid 306 through 309 Processing sheet with id=AJ8, first strand: chain 'R' and resid 377 through 378 Processing sheet with id=AJ9, first strand: chain 'R' and resid 476 through 477 removed outlier: 3.632A pdb=" N ARG R 476 " --> pdb=" O ALA R 494 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'R' and resid 497 through 499 removed outlier: 3.774A pdb=" N ASP R 498 " --> pdb=" O VAL R 506 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'T' and resid 77 through 82 Processing sheet with id=AK3, first strand: chain 'T' and resid 142 through 149 removed outlier: 3.691A pdb=" N ILE T 149 " --> pdb=" O ALA T 125 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ALA T 125 " --> pdb=" O ILE T 149 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'T' and resid 156 through 158 Processing sheet with id=AK5, first strand: chain 'T' and resid 156 through 158 removed outlier: 6.251A pdb=" N GLN T 236 " --> pdb=" O LYS T 265 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS T 265 " --> pdb=" O GLN T 236 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL T 276 " --> pdb=" O ILE T 293 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ILE T 280 " --> pdb=" O ASP T 289 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ASP T 289 " --> pdb=" O ILE T 280 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'T' and resid 306 through 309 Processing sheet with id=AK7, first strand: chain 'T' and resid 390 through 391 removed outlier: 4.641A pdb=" N ALA T 390 " --> pdb=" O PHE T 350 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'T' and resid 377 through 378 Processing sheet with id=AK9, first strand: chain 'T' and resid 476 through 477 removed outlier: 3.622A pdb=" N ARG T 476 " --> pdb=" O ALA T 494 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'T' and resid 497 through 499 removed outlier: 3.902A pdb=" N ASP T 498 " --> pdb=" O VAL T 506 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'W' and resid 77 through 82 Processing sheet with id=AL3, first strand: chain 'W' and resid 142 through 149 removed outlier: 3.705A pdb=" N ILE W 149 " --> pdb=" O ALA W 125 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA W 125 " --> pdb=" O ILE W 149 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'W' and resid 156 through 158 Processing sheet with id=AL5, first strand: chain 'W' and resid 156 through 158 removed outlier: 4.454A pdb=" N VAL W 276 " --> pdb=" O ILE W 293 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ILE W 280 " --> pdb=" O ASP W 289 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP W 289 " --> pdb=" O ILE W 280 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'W' and resid 306 through 309 Processing sheet with id=AL7, first strand: chain 'W' and resid 377 through 378 Processing sheet with id=AL8, first strand: chain 'W' and resid 476 through 477 removed outlier: 3.639A pdb=" N ARG W 476 " --> pdb=" O ALA W 494 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'W' and resid 497 through 499 removed outlier: 3.763A pdb=" N ASP W 498 " --> pdb=" O VAL W 506 " (cutoff:3.500A) 3888 hydrogen bonds defined for protein. 11373 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: 25.03 Time building geometry restraints manager: 22.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 12896 1.32 - 1.44: 19165 1.44 - 1.57: 41691 1.57 - 1.69: 0 1.69 - 1.82: 588 Bond restraints: 74340 Sorted by residual: bond pdb=" C PRO B 243 " pdb=" O PRO B 243 " ideal model delta sigma weight residual 1.235 1.195 0.040 1.30e-02 5.92e+03 9.53e+00 bond pdb=" N PRO T 243 " pdb=" CA PRO T 243 " ideal model delta sigma weight residual 1.469 1.432 0.037 1.28e-02 6.10e+03 8.43e+00 bond pdb=" N PRO N 243 " pdb=" CA PRO N 243 " ideal model delta sigma weight residual 1.469 1.432 0.037 1.28e-02 6.10e+03 8.23e+00 bond pdb=" N PRO L 243 " pdb=" CA PRO L 243 " ideal model delta sigma weight residual 1.469 1.432 0.036 1.28e-02 6.10e+03 8.12e+00 bond pdb=" C PRO H 243 " pdb=" O PRO H 243 " ideal model delta sigma weight residual 1.235 1.198 0.037 1.30e-02 5.92e+03 8.09e+00 ... (remaining 74335 not shown) Histogram of bond angle deviations from ideal: 98.40 - 105.54: 1501 105.54 - 112.67: 38351 112.67 - 119.80: 24886 119.80 - 126.93: 35125 126.93 - 134.06: 937 Bond angle restraints: 100800 Sorted by residual: angle pdb=" C GLU F 585 " pdb=" N THR F 586 " pdb=" CA THR F 586 " ideal model delta sigma weight residual 120.49 131.43 -10.94 1.42e+00 4.96e-01 5.94e+01 angle pdb=" N GLU F 296 " pdb=" CA GLU F 296 " pdb=" C GLU F 296 " ideal model delta sigma weight residual 113.02 104.62 8.40 1.49e+00 4.50e-01 3.18e+01 angle pdb=" N LEU D 622 " pdb=" CA LEU D 622 " pdb=" C LEU D 622 " ideal model delta sigma weight residual 111.14 105.55 5.59 1.08e+00 8.57e-01 2.68e+01 angle pdb=" N LEU M 40 " pdb=" CA LEU M 40 " pdb=" C LEU M 40 " ideal model delta sigma weight residual 111.28 105.89 5.39 1.09e+00 8.42e-01 2.45e+01 angle pdb=" N LEU B 622 " pdb=" CA LEU B 622 " pdb=" C LEU B 622 " ideal model delta sigma weight residual 111.36 105.97 5.39 1.09e+00 8.42e-01 2.44e+01 ... (remaining 100795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 37757 17.99 - 35.99: 4977 35.99 - 53.98: 1890 53.98 - 71.98: 351 71.98 - 89.97: 193 Dihedral angle restraints: 45168 sinusoidal: 18420 harmonic: 26748 Sorted by residual: dihedral pdb=" CD ARG L 171 " pdb=" NE ARG L 171 " pdb=" CZ ARG L 171 " pdb=" NH1 ARG L 171 " ideal model delta sinusoidal sigma weight residual 0.00 76.15 -76.15 1 1.00e+01 1.00e-02 7.30e+01 dihedral pdb=" CA GLU L 621 " pdb=" C GLU L 621 " pdb=" N LEU L 622 " pdb=" CA LEU L 622 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ASP J 561 " pdb=" C ASP J 561 " pdb=" N GLY J 562 " pdb=" CA GLY J 562 " ideal model delta harmonic sigma weight residual 180.00 161.08 18.92 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 45165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 9829 0.067 - 0.134: 1012 0.134 - 0.201: 62 0.201 - 0.267: 3 0.267 - 0.334: 2 Chirality restraints: 10908 Sorted by residual: chirality pdb=" CA GLU F 296 " pdb=" N GLU F 296 " pdb=" C GLU F 296 " pdb=" CB GLU F 296 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA LEU D 622 " pdb=" N LEU D 622 " pdb=" C LEU D 622 " pdb=" CB LEU D 622 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA LEU B 622 " pdb=" N LEU B 622 " pdb=" C LEU B 622 " pdb=" CB LEU B 622 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 10905 not shown) Planarity restraints: 13344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 171 " -1.071 9.50e-02 1.11e+02 4.80e-01 1.39e+02 pdb=" NE ARG L 171 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG L 171 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG L 171 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG L 171 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG W 249 " -0.520 9.50e-02 1.11e+02 2.33e-01 3.33e+01 pdb=" NE ARG W 249 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG W 249 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG W 249 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG W 249 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 621 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.27e+00 pdb=" C GLU B 621 " -0.053 2.00e-02 2.50e+03 pdb=" O GLU B 621 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU B 622 " 0.018 2.00e-02 2.50e+03 ... (remaining 13341 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 5474 2.74 - 3.28: 70336 3.28 - 3.82: 124366 3.82 - 4.36: 147587 4.36 - 4.90: 259624 Nonbonded interactions: 607387 Sorted by model distance: nonbonded pdb=" OH TYR F 556 " pdb=" OG1 THR H 542 " model vdw 2.196 2.440 nonbonded pdb=" NZ LYS V 16 " pdb=" OD2 ASP X 39 " model vdw 2.198 2.520 nonbonded pdb=" OD1 ASP R 367 " pdb=" NH2 ARG S 125 " model vdw 2.218 2.520 nonbonded pdb=" NZ LYS K 16 " pdb=" OD2 ASP O 39 " model vdw 2.220 2.520 nonbonded pdb=" OD1 ASN A 182 " pdb=" NH2 ARG B 171 " model vdw 2.222 2.520 ... (remaining 607382 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 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'W' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'V' selection = chain 'X' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.460 Construct map_model_manager: 0.030 Extract box with map and model: 17.340 Check model and map are aligned: 0.810 Set scattering table: 0.510 Process input model: 139.400 Find NCS groups from input model: 3.700 Set up NCS constraints: 0.510 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 174.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 0.045 74340 Z= 0.193 Angle : 0.578 13.374 100800 Z= 0.308 Chirality : 0.042 0.334 10908 Planarity : 0.006 0.480 13344 Dihedral : 19.508 89.974 27888 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.55 % Allowed : 29.60 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.18 (0.09), residues: 9024 helix: 2.28 (0.08), residues: 4104 sheet: -0.52 (0.16), residues: 984 loop : -0.47 (0.11), residues: 3936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 126 HIS 0.008 0.001 HIS P 172 PHE 0.027 0.001 PHE Q 84 TYR 0.043 0.001 TYR D 191 ARG 0.014 0.000 ARG W 511 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1926 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 1649 time to evaluate : 6.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 277 outliers final: 230 residues processed: 1875 average time/residue: 1.4486 time to fit residues: 3585.3169 Evaluate side-chains 1852 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1622 time to evaluate : 6.241 Switching outliers to nearest non-outliers outliers start: 230 outliers final: 210 residues processed: 29 average time/residue: 0.7205 time to fit residues: 42.8822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 759 optimal weight: 3.9990 chunk 682 optimal weight: 2.9990 chunk 378 optimal weight: 4.9990 chunk 233 optimal weight: 0.0670 chunk 460 optimal weight: 1.9990 chunk 364 optimal weight: 2.9990 chunk 705 optimal weight: 3.9990 chunk 272 optimal weight: 3.9990 chunk 428 optimal weight: 3.9990 chunk 525 optimal weight: 5.9990 chunk 817 optimal weight: 4.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 450 GLN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN B 141 ASN B 450 GLN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 GLN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 ASN F 450 GLN ** F 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN H 141 ASN H 450 GLN H 525 GLN ** H 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 525 GLN ** J 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 450 GLN L 525 GLN ** L 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 74 ASN N 141 ASN N 450 GLN P 450 GLN ** P 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 203 ASN R 450 GLN ** R 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 598 GLN T 74 ASN T 141 ASN T 450 GLN T 525 GLN W 203 ASN W 450 GLN ** W 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 74340 Z= 0.426 Angle : 0.578 12.063 100800 Z= 0.302 Chirality : 0.045 0.191 10908 Planarity : 0.005 0.077 13344 Dihedral : 4.158 22.332 9972 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 7.06 % Allowed : 25.62 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.09), residues: 9024 helix: 2.42 (0.08), residues: 4152 sheet: -0.53 (0.16), residues: 924 loop : -0.53 (0.10), residues: 3948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 307 HIS 0.005 0.001 HIS L 177 PHE 0.037 0.002 PHE V 84 TYR 0.013 0.002 TYR S 48 ARG 0.007 0.001 ARG T 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2220 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 551 poor density : 1669 time to evaluate : 6.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 551 outliers final: 310 residues processed: 2033 average time/residue: 1.5341 time to fit residues: 4079.1680 Evaluate side-chains 1930 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 1620 time to evaluate : 6.266 Switching outliers to nearest non-outliers outliers start: 310 outliers final: 228 residues processed: 86 average time/residue: 1.0890 time to fit residues: 142.7399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 454 optimal weight: 0.9990 chunk 253 optimal weight: 4.9990 chunk 680 optimal weight: 0.6980 chunk 556 optimal weight: 0.9990 chunk 225 optimal weight: 3.9990 chunk 818 optimal weight: 0.8980 chunk 884 optimal weight: 8.9990 chunk 729 optimal weight: 5.9990 chunk 811 optimal weight: 1.9990 chunk 279 optimal weight: 4.9990 chunk 656 optimal weight: 8.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 450 GLN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN B 450 GLN B 525 GLN D 40 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 GLN E 144 ASN F 203 ASN F 450 GLN G 147 HIS H 361 HIS H 450 GLN H 525 GLN ** J 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 450 GLN J 525 GLN ** J 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 144 ASN ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 450 GLN L 525 GLN L 573 ASN ** L 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 144 ASN N 450 GLN P 450 GLN P 525 GLN ** P 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 144 ASN R 203 ASN R 450 GLN ** R 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 450 GLN T 525 GLN W 203 ASN W 450 GLN ** W 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 74340 Z= 0.229 Angle : 0.501 11.063 100800 Z= 0.260 Chirality : 0.041 0.167 10908 Planarity : 0.004 0.064 13344 Dihedral : 3.982 19.555 9972 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 6.36 % Allowed : 26.72 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.09), residues: 9024 helix: 2.75 (0.08), residues: 4152 sheet: -0.53 (0.16), residues: 924 loop : -0.49 (0.10), residues: 3948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 126 HIS 0.005 0.001 HIS D 177 PHE 0.029 0.002 PHE I 84 TYR 0.021 0.001 TYR P 191 ARG 0.008 0.000 ARG N 274 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2183 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 496 poor density : 1687 time to evaluate : 6.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 496 outliers final: 292 residues processed: 2023 average time/residue: 1.4841 time to fit residues: 3962.9297 Evaluate side-chains 1958 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 1666 time to evaluate : 6.277 Switching outliers to nearest non-outliers outliers start: 292 outliers final: 227 residues processed: 69 average time/residue: 1.0163 time to fit residues: 111.5398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 808 optimal weight: 10.0000 chunk 615 optimal weight: 0.9980 chunk 424 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 390 optimal weight: 0.9980 chunk 549 optimal weight: 5.9990 chunk 821 optimal weight: 2.9990 chunk 869 optimal weight: 0.9990 chunk 429 optimal weight: 0.3980 chunk 778 optimal weight: 2.9990 chunk 234 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 450 GLN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 GLN B 525 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 ASN F 203 ASN F 450 GLN H 450 GLN H 525 GLN ** J 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 450 GLN ** J 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 144 ASN ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 573 ASN ** L 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 144 ASN N 450 GLN ** N 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 297 HIS ** P 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 142 ASN Q 144 ASN R 203 ASN R 450 GLN ** R 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 450 GLN T 525 GLN W 203 ASN W 205 ASN W 450 GLN ** W 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 74340 Z= 0.196 Angle : 0.494 10.502 100800 Z= 0.255 Chirality : 0.040 0.213 10908 Planarity : 0.004 0.073 13344 Dihedral : 3.876 19.286 9972 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 5.91 % Allowed : 27.51 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.09), residues: 9024 helix: 2.91 (0.08), residues: 4152 sheet: -0.57 (0.16), residues: 984 loop : -0.46 (0.11), residues: 3888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 126 HIS 0.003 0.001 HIS T 177 PHE 0.028 0.001 PHE V 84 TYR 0.012 0.001 TYR L 191 ARG 0.008 0.000 ARG H 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2173 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 461 poor density : 1712 time to evaluate : 6.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 461 outliers final: 280 residues processed: 2043 average time/residue: 1.4540 time to fit residues: 3957.6373 Evaluate side-chains 1945 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 1665 time to evaluate : 6.313 Switching outliers to nearest non-outliers outliers start: 280 outliers final: 226 residues processed: 61 average time/residue: 1.0707 time to fit residues: 103.3994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 724 optimal weight: 1.9990 chunk 493 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 647 optimal weight: 4.9990 chunk 358 optimal weight: 5.9990 chunk 742 optimal weight: 6.9990 chunk 601 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 444 optimal weight: 3.9990 chunk 780 optimal weight: 0.9990 chunk 219 optimal weight: 0.3980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 450 GLN ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 ASN F 203 ASN F 450 GLN H 525 GLN ** J 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 144 ASN ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 573 ASN ** L 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 142 ASN ** N 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 142 ASN Q 144 ASN R 203 ASN R 450 GLN ** R 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 525 GLN W 203 ASN W 450 GLN ** W 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 74340 Z= 0.253 Angle : 0.523 10.395 100800 Z= 0.269 Chirality : 0.042 0.208 10908 Planarity : 0.004 0.067 13344 Dihedral : 3.925 19.434 9972 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.88 % Allowed : 27.90 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.09), residues: 9024 helix: 2.86 (0.08), residues: 4152 sheet: -0.59 (0.16), residues: 984 loop : -0.48 (0.11), residues: 3888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 126 HIS 0.003 0.001 HIS L 177 PHE 0.030 0.002 PHE V 84 TYR 0.011 0.001 TYR P 191 ARG 0.008 0.000 ARG B 274 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2139 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 459 poor density : 1680 time to evaluate : 6.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 459 outliers final: 304 residues processed: 1979 average time/residue: 1.4528 time to fit residues: 3809.0694 Evaluate side-chains 1953 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 1649 time to evaluate : 6.307 Switching outliers to nearest non-outliers outliers start: 304 outliers final: 234 residues processed: 74 average time/residue: 1.0949 time to fit residues: 124.8766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 292 optimal weight: 5.9990 chunk 783 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 510 optimal weight: 0.6980 chunk 214 optimal weight: 1.9990 chunk 870 optimal weight: 20.0000 chunk 722 optimal weight: 0.8980 chunk 403 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 288 optimal weight: 0.9980 chunk 457 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 450 GLN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 GLN B 525 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 ASN E 144 ASN F 203 ASN F 450 GLN ** F 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 450 GLN H 525 GLN ** J 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 450 GLN J 525 GLN ** J 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 ASN K 144 ASN ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 573 ASN ** L 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 142 ASN M 144 ASN N 591 GLN P 525 GLN ** P 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 142 ASN Q 144 ASN R 203 ASN R 450 GLN T 450 GLN T 525 GLN W 203 ASN W 450 GLN ** W 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 74340 Z= 0.195 Angle : 0.505 10.726 100800 Z= 0.258 Chirality : 0.041 0.188 10908 Planarity : 0.004 0.060 13344 Dihedral : 3.842 18.813 9972 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.92 % Allowed : 29.03 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.09), residues: 9024 helix: 2.96 (0.08), residues: 4152 sheet: -0.55 (0.16), residues: 984 loop : -0.44 (0.11), residues: 3888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 126 HIS 0.003 0.001 HIS P 172 PHE 0.028 0.001 PHE a 84 TYR 0.011 0.001 TYR J 191 ARG 0.008 0.000 ARG N 274 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2082 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 384 poor density : 1698 time to evaluate : 6.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 384 outliers final: 270 residues processed: 1982 average time/residue: 1.4773 time to fit residues: 3890.7718 Evaluate side-chains 1934 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 1664 time to evaluate : 6.297 Switching outliers to nearest non-outliers outliers start: 270 outliers final: 228 residues processed: 50 average time/residue: 1.0254 time to fit residues: 84.7071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 839 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 496 optimal weight: 4.9990 chunk 635 optimal weight: 2.9990 chunk 492 optimal weight: 0.8980 chunk 733 optimal weight: 1.9990 chunk 486 optimal weight: 0.8980 chunk 867 optimal weight: 2.9990 chunk 542 optimal weight: 0.6980 chunk 528 optimal weight: 1.9990 chunk 400 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 450 GLN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 GLN B 525 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 ASN F 450 GLN ** F 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 525 GLN ** J 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 525 GLN ** J 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 573 ASN ** L 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 144 ASN P 525 GLN ** P 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 144 ASN R 203 ASN R 450 GLN T 525 GLN ** T 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 203 ASN W 450 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 74340 Z= 0.226 Angle : 0.518 11.351 100800 Z= 0.264 Chirality : 0.041 0.188 10908 Planarity : 0.004 0.063 13344 Dihedral : 3.867 18.924 9972 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.83 % Allowed : 28.82 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.09), residues: 9024 helix: 2.93 (0.08), residues: 4152 sheet: -0.55 (0.16), residues: 984 loop : -0.45 (0.11), residues: 3888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 126 HIS 0.003 0.001 HIS L 177 PHE 0.029 0.002 PHE a 84 TYR 0.019 0.001 TYR P 191 ARG 0.007 0.000 ARG N 274 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2045 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 377 poor density : 1668 time to evaluate : 6.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 377 outliers final: 279 residues processed: 1933 average time/residue: 1.4658 time to fit residues: 3753.6196 Evaluate side-chains 1921 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 1642 time to evaluate : 6.267 Switching outliers to nearest non-outliers outliers start: 279 outliers final: 225 residues processed: 62 average time/residue: 1.0142 time to fit residues: 101.0602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 536 optimal weight: 1.9990 chunk 346 optimal weight: 4.9990 chunk 518 optimal weight: 0.6980 chunk 261 optimal weight: 0.5980 chunk 170 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 551 optimal weight: 3.9990 chunk 590 optimal weight: 0.9980 chunk 428 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 681 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 450 GLN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 ASN E 144 ASN F 203 ASN F 450 GLN ** F 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 525 GLN ** J 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 525 GLN ** J 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 144 ASN ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 573 ASN ** L 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 144 ASN P 525 GLN ** P 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 144 ASN R 203 ASN R 450 GLN T 525 GLN ** T 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 203 ASN W 450 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 74340 Z= 0.223 Angle : 0.522 14.745 100800 Z= 0.265 Chirality : 0.041 0.188 10908 Planarity : 0.004 0.058 13344 Dihedral : 3.862 18.780 9972 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.32 % Allowed : 29.51 % Favored : 66.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.70 (0.09), residues: 9024 helix: 2.94 (0.08), residues: 4152 sheet: -0.57 (0.16), residues: 984 loop : -0.45 (0.11), residues: 3888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 126 HIS 0.003 0.001 HIS L 177 PHE 0.029 0.002 PHE S 84 TYR 0.020 0.001 TYR P 191 ARG 0.007 0.000 ARG H 274 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2004 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 1667 time to evaluate : 6.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 337 outliers final: 272 residues processed: 1913 average time/residue: 1.4834 time to fit residues: 3764.0803 Evaluate side-chains 1907 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1635 time to evaluate : 6.270 Switching outliers to nearest non-outliers outliers start: 272 outliers final: 226 residues processed: 55 average time/residue: 1.0730 time to fit residues: 94.3521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 789 optimal weight: 2.9990 chunk 831 optimal weight: 2.9990 chunk 758 optimal weight: 2.9990 chunk 808 optimal weight: 5.9990 chunk 830 optimal weight: 0.9990 chunk 486 optimal weight: 0.6980 chunk 352 optimal weight: 2.9990 chunk 634 optimal weight: 0.3980 chunk 248 optimal weight: 0.0030 chunk 730 optimal weight: 0.4980 chunk 764 optimal weight: 3.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 450 GLN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 ASN F 450 GLN ** F 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 450 GLN H 525 GLN ** J 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 525 GLN J 573 ASN ** J 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 144 ASN ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 573 ASN ** L 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 182 ASN N 450 GLN ** P 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 525 GLN ** P 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 144 ASN R 203 ASN R 450 GLN T 525 GLN ** T 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 203 ASN W 205 ASN W 450 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 74340 Z= 0.161 Angle : 0.508 16.414 100800 Z= 0.256 Chirality : 0.040 0.185 10908 Planarity : 0.004 0.054 13344 Dihedral : 3.732 18.655 9972 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.63 % Allowed : 30.29 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.09), residues: 9024 helix: 3.05 (0.08), residues: 4164 sheet: -0.48 (0.16), residues: 984 loop : -0.39 (0.11), residues: 3876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 126 HIS 0.002 0.000 HIS T 172 PHE 0.028 0.001 PHE S 84 TYR 0.014 0.001 TYR P 191 ARG 0.008 0.000 ARG R 511 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1997 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 1714 time to evaluate : 6.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 283 outliers final: 228 residues processed: 1952 average time/residue: 1.4511 time to fit residues: 3776.0035 Evaluate side-chains 1885 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1657 time to evaluate : 6.257 Switching outliers to nearest non-outliers outliers start: 228 outliers final: 217 residues processed: 23 average time/residue: 0.7592 time to fit residues: 37.1407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 805 optimal weight: 0.9980 chunk 530 optimal weight: 0.0980 chunk 854 optimal weight: 1.9990 chunk 521 optimal weight: 0.8980 chunk 405 optimal weight: 1.9990 chunk 594 optimal weight: 0.5980 chunk 896 optimal weight: 9.9990 chunk 825 optimal weight: 5.9990 chunk 713 optimal weight: 0.0570 chunk 74 optimal weight: 0.3980 chunk 551 optimal weight: 5.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 203 ASN A 450 GLN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN B 525 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 ASN F 203 ASN F 450 GLN ** F 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 525 GLN J 40 GLN ** J 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 573 ASN ** L 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 144 ASN N 525 GLN ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 203 ASN R 450 GLN T 525 GLN ** T 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 161 ASN W 203 ASN W 450 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 74340 Z= 0.153 Angle : 0.512 14.841 100800 Z= 0.257 Chirality : 0.040 0.216 10908 Planarity : 0.004 0.051 13344 Dihedral : 3.657 18.513 9972 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.23 % Allowed : 30.77 % Favored : 66.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.09), residues: 9024 helix: 3.13 (0.08), residues: 4164 sheet: -0.43 (0.16), residues: 984 loop : -0.35 (0.11), residues: 3876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 126 HIS 0.002 0.000 HIS B 172 PHE 0.027 0.001 PHE S 84 TYR 0.010 0.001 TYR P 191 ARG 0.007 0.000 ARG P 274 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1958 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 1706 time to evaluate : 6.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 252 outliers final: 222 residues processed: 1925 average time/residue: 1.4672 time to fit residues: 3757.6884 Evaluate side-chains 1882 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1660 time to evaluate : 5.636 Switching outliers to nearest non-outliers outliers start: 222 outliers final: 208 residues processed: 23 average time/residue: 0.6855 time to fit residues: 33.4195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 437 optimal weight: 0.9990 chunk 567 optimal weight: 4.9990 chunk 760 optimal weight: 0.8980 chunk 218 optimal weight: 0.7980 chunk 658 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 715 optimal weight: 0.8980 chunk 299 optimal weight: 3.9990 chunk 734 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 450 GLN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 ASN F 450 GLN ** F 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 525 GLN ** J 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 144 ASN L 40 GLN ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 573 ASN ** L 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 525 GLN ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 525 GLN ** P 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 203 ASN R 450 GLN T 525 GLN ** T 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 203 ASN W 450 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.137248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.100133 restraints weight = 85257.787| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.08 r_work: 0.2928 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 74340 Z= 0.208 Angle : 0.533 15.741 100800 Z= 0.269 Chirality : 0.041 0.198 10908 Planarity : 0.004 0.047 13344 Dihedral : 3.732 18.834 9972 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.26 % Allowed : 30.79 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.09), residues: 9024 helix: 3.08 (0.08), residues: 4152 sheet: -0.48 (0.16), residues: 984 loop : -0.36 (0.11), residues: 3888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 211 HIS 0.004 0.001 HIS R 177 PHE 0.029 0.001 PHE a 84 TYR 0.017 0.001 TYR P 556 ARG 0.007 0.000 ARG P 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 45234.42 seconds wall clock time: 773 minutes 15.45 seconds (46395.45 seconds total)