Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 3 21:21:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdi_33148/07_2023/7xdi_33148.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdi_33148/07_2023/7xdi_33148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdi_33148/07_2023/7xdi_33148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdi_33148/07_2023/7xdi_33148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdi_33148/07_2023/7xdi_33148.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdi_33148/07_2023/7xdi_33148.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.048 sd= 5.514 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 35777 2.51 5 N 8218 2.21 5 O 9506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "E GLU 70": "OE1" <-> "OE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 58": "OE1" <-> "OE2" Residue "F ASP 69": "OD1" <-> "OD2" Residue "F TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 599": "OE1" <-> "OE2" Residue "F GLU 601": "OE1" <-> "OE2" Residue "F GLU 979": "OE1" <-> "OE2" Residue "F TYR 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 58": "OE1" <-> "OE2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "K PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 58": "OE1" <-> "OE2" Residue "L ASP 69": "OD1" <-> "OD2" Residue "L TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 599": "OE1" <-> "OE2" Residue "L GLU 601": "OE1" <-> "OE2" Residue "L GLU 979": "OE1" <-> "OE2" Residue "L TYR 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 58": "OE1" <-> "OE2" Residue "Q GLU 70": "OE1" <-> "OE2" Residue "Q GLU 73": "OE1" <-> "OE2" Residue "Q PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 58": "OE1" <-> "OE2" Residue "R ASP 69": "OD1" <-> "OD2" Residue "R TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 599": "OE1" <-> "OE2" Residue "R GLU 601": "OE1" <-> "OE2" Residue "R GLU 979": "OE1" <-> "OE2" Residue "R TYR 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 58": "OE1" <-> "OE2" Residue "W GLU 70": "OE1" <-> "OE2" Residue "W GLU 73": "OE1" <-> "OE2" Residue "W PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 58": "OE1" <-> "OE2" Residue "X ASP 69": "OD1" <-> "OD2" Residue "X TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 599": "OE1" <-> "OE2" Residue "X GLU 601": "OE1" <-> "OE2" Residue "X GLU 979": "OE1" <-> "OE2" Residue "X TYR 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 58": "OE1" <-> "OE2" Residue "2 GLU 70": "OE1" <-> "OE2" Residue "2 GLU 73": "OE1" <-> "OE2" Residue "2 PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 58": "OE1" <-> "OE2" Residue "3 ASP 69": "OD1" <-> "OD2" Residue "3 TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 599": "OE1" <-> "OE2" Residue "3 GLU 601": "OE1" <-> "OE2" Residue "3 GLU 979": "OE1" <-> "OE2" Residue "3 TYR 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 58": "OE1" <-> "OE2" Residue "8 GLU 70": "OE1" <-> "OE2" Residue "8 GLU 73": "OE1" <-> "OE2" Residue "8 PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 58": "OE1" <-> "OE2" Residue "9 ASP 69": "OD1" <-> "OD2" Residue "9 TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 599": "OE1" <-> "OE2" Residue "9 GLU 601": "OE1" <-> "OE2" Residue "9 GLU 979": "OE1" <-> "OE2" Residue "9 TYR 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 58": "OE1" <-> "OE2" Residue "e GLU 70": "OE1" <-> "OE2" Residue "e GLU 73": "OE1" <-> "OE2" Residue "e PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 58": "OE1" <-> "OE2" Residue "f ASP 69": "OD1" <-> "OD2" Residue "f TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 599": "OE1" <-> "OE2" Residue "f GLU 601": "OE1" <-> "OE2" Residue "f GLU 979": "OE1" <-> "OE2" Residue "f TYR 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 53669 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 516 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "B" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 516 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "C" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 516 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "D" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 996 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "E" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1443 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 14, 'TRANS': 170} Chain: "F" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3680 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 18, 'TRANS': 437} Chain breaks: 4 Chain: "G" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 516 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "H" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 516 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "I" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 516 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "J" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 996 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "K" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1443 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 14, 'TRANS': 170} Chain: "L" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3680 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 18, 'TRANS': 437} Chain breaks: 4 Chain: "M" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 516 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "N" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 516 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "O" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 516 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "P" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 996 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "Q" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1443 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 14, 'TRANS': 170} Chain: "R" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3680 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 18, 'TRANS': 437} Chain breaks: 4 Chain: "S" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 516 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "T" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 516 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "U" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 516 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "V" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 996 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "W" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1443 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 14, 'TRANS': 170} Chain: "X" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3680 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 18, 'TRANS': 437} Chain breaks: 4 Chain: "Y" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 516 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "Z" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 516 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "0" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 516 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "1" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 996 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "2" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1443 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 14, 'TRANS': 170} Chain: "3" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3680 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 18, 'TRANS': 437} Chain breaks: 4 Chain: "4" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 516 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "5" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 516 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "6" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 516 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "7" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 996 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "8" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1443 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 14, 'TRANS': 170} Chain: "9" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3680 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 18, 'TRANS': 437} Chain breaks: 4 Chain: "a" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 516 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "b" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 516 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "c" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 516 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "d" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 996 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "e" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1443 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 14, 'TRANS': 170} Chain: "f" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3680 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 18, 'TRANS': 437} Chain breaks: 4 Time building chain proxies: 18.19, per 1000 atoms: 0.34 Number of scatterers: 53669 At special positions: 0 Unit cell: (196.85, 196.85, 135.89, 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 168 16.00 O 9506 8.00 N 8218 7.00 C 35777 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: 16.96 Conformation dependent library (CDL) restraints added in 5.8 seconds 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12824 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 56 sheets defined 62.2% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 15 through 32 Processing helix chain 'A' and resid 32 through 45 removed outlier: 3.770A pdb=" N ILE A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 83 Proline residue: A 63 - end of helix Proline residue: A 74 - end of helix removed outlier: 3.665A pdb=" N ARG A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 45 Proline residue: B 34 - end of helix Processing helix chain 'B' and resid 53 through 82 Proline residue: B 63 - end of helix Proline residue: B 74 - end of helix Processing helix chain 'C' and resid 16 through 45 removed outlier: 3.638A pdb=" N PHE C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Proline residue: C 34 - end of helix Processing helix chain 'C' and resid 53 through 83 Proline residue: C 63 - end of helix Proline residue: C 74 - end of helix Processing helix chain 'D' and resid 3 through 20 Processing helix chain 'D' and resid 36 through 44 Processing helix chain 'D' and resid 60 through 96 Processing helix chain 'D' and resid 101 through 125 Processing helix chain 'E' and resid 136 through 159 Processing helix chain 'E' and resid 160 through 178 removed outlier: 3.825A pdb=" N ALA E 165 " --> pdb=" O PRO E 161 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE E 178 " --> pdb=" O ILE E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 204 removed outlier: 3.625A pdb=" N VAL E 188 " --> pdb=" O TYR E 184 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA E 194 " --> pdb=" O LEU E 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 45 Processing helix chain 'F' and resid 67 through 79 Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'F' and resid 85 through 99 Processing helix chain 'F' and resid 598 through 612 removed outlier: 3.668A pdb=" N TYR F 612 " --> pdb=" O LEU F 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 636 removed outlier: 3.560A pdb=" N TYR F 635 " --> pdb=" O GLN F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 658 Processing helix chain 'F' and resid 660 through 677 removed outlier: 4.502A pdb=" N SER F 664 " --> pdb=" O ASN F 660 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN F 665 " --> pdb=" O THR F 661 " (cutoff:3.500A) Processing helix chain 'F' and resid 903 through 921 Processing helix chain 'F' and resid 922 through 936 removed outlier: 3.855A pdb=" N LEU F 926 " --> pdb=" O ASN F 922 " (cutoff:3.500A) Processing helix chain 'F' and resid 975 through 989 Processing helix chain 'F' and resid 990 through 1003 Processing helix chain 'F' and resid 1030 through 1046 Processing helix chain 'F' and resid 1164 through 1187 Processing helix chain 'F' and resid 1189 through 1207 removed outlier: 3.600A pdb=" N THR F1193 " --> pdb=" O ASN F1189 " (cutoff:3.500A) Processing helix chain 'F' and resid 1211 through 1233 Processing helix chain 'G' and resid 15 through 32 Processing helix chain 'G' and resid 32 through 45 removed outlier: 3.770A pdb=" N ILE G 36 " --> pdb=" O LEU G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 83 Proline residue: G 63 - end of helix Proline residue: G 74 - end of helix removed outlier: 3.665A pdb=" N ARG G 83 " --> pdb=" O TYR G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 45 Proline residue: H 34 - end of helix Processing helix chain 'H' and resid 53 through 82 Proline residue: H 63 - end of helix Proline residue: H 74 - end of helix Processing helix chain 'I' and resid 16 through 45 removed outlier: 3.638A pdb=" N PHE I 23 " --> pdb=" O LEU I 19 " (cutoff:3.500A) Proline residue: I 34 - end of helix Processing helix chain 'I' and resid 53 through 83 Proline residue: I 63 - end of helix Proline residue: I 74 - end of helix Processing helix chain 'J' and resid 3 through 20 Processing helix chain 'J' and resid 36 through 44 Processing helix chain 'J' and resid 60 through 96 Processing helix chain 'J' and resid 101 through 125 Processing helix chain 'K' and resid 136 through 159 Processing helix chain 'K' and resid 160 through 178 removed outlier: 3.824A pdb=" N ALA K 165 " --> pdb=" O PRO K 161 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE K 178 " --> pdb=" O ILE K 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 204 removed outlier: 3.624A pdb=" N VAL K 188 " --> pdb=" O TYR K 184 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA K 194 " --> pdb=" O LEU K 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 45 Processing helix chain 'L' and resid 67 through 79 Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'L' and resid 85 through 99 Processing helix chain 'L' and resid 598 through 612 removed outlier: 3.669A pdb=" N TYR L 612 " --> pdb=" O LEU L 608 " (cutoff:3.500A) Processing helix chain 'L' and resid 614 through 636 removed outlier: 3.560A pdb=" N TYR L 635 " --> pdb=" O GLN L 631 " (cutoff:3.500A) Processing helix chain 'L' and resid 640 through 658 Processing helix chain 'L' and resid 660 through 677 removed outlier: 4.502A pdb=" N SER L 664 " --> pdb=" O ASN L 660 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN L 665 " --> pdb=" O THR L 661 " (cutoff:3.500A) Processing helix chain 'L' and resid 903 through 921 Processing helix chain 'L' and resid 922 through 936 removed outlier: 3.854A pdb=" N LEU L 926 " --> pdb=" O ASN L 922 " (cutoff:3.500A) Processing helix chain 'L' and resid 975 through 989 Processing helix chain 'L' and resid 990 through 1003 Processing helix chain 'L' and resid 1030 through 1046 Processing helix chain 'L' and resid 1164 through 1187 Processing helix chain 'L' and resid 1189 through 1207 removed outlier: 3.600A pdb=" N THR L1193 " --> pdb=" O ASN L1189 " (cutoff:3.500A) Processing helix chain 'L' and resid 1211 through 1233 Processing helix chain 'M' and resid 15 through 32 Processing helix chain 'M' and resid 32 through 45 removed outlier: 3.769A pdb=" N ILE M 36 " --> pdb=" O LEU M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 83 Proline residue: M 63 - end of helix Proline residue: M 74 - end of helix removed outlier: 3.664A pdb=" N ARG M 83 " --> pdb=" O TYR M 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 45 Proline residue: N 34 - end of helix Processing helix chain 'N' and resid 53 through 82 Proline residue: N 63 - end of helix Proline residue: N 74 - end of helix Processing helix chain 'O' and resid 16 through 45 removed outlier: 3.638A pdb=" N PHE O 23 " --> pdb=" O LEU O 19 " (cutoff:3.500A) Proline residue: O 34 - end of helix Processing helix chain 'O' and resid 53 through 83 Proline residue: O 63 - end of helix Proline residue: O 74 - end of helix Processing helix chain 'P' and resid 3 through 20 Processing helix chain 'P' and resid 36 through 44 Processing helix chain 'P' and resid 60 through 96 Processing helix chain 'P' and resid 101 through 125 Processing helix chain 'Q' and resid 136 through 159 Processing helix chain 'Q' and resid 160 through 178 removed outlier: 3.825A pdb=" N ALA Q 165 " --> pdb=" O PRO Q 161 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE Q 178 " --> pdb=" O ILE Q 174 " (cutoff:3.500A) Processing helix chain 'Q' and resid 184 through 204 removed outlier: 3.625A pdb=" N VAL Q 188 " --> pdb=" O TYR Q 184 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA Q 194 " --> pdb=" O LEU Q 190 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 45 Processing helix chain 'R' and resid 67 through 79 Processing helix chain 'R' and resid 80 through 82 No H-bonds generated for 'chain 'R' and resid 80 through 82' Processing helix chain 'R' and resid 85 through 99 Processing helix chain 'R' and resid 598 through 612 removed outlier: 3.668A pdb=" N TYR R 612 " --> pdb=" O LEU R 608 " (cutoff:3.500A) Processing helix chain 'R' and resid 614 through 636 removed outlier: 3.560A pdb=" N TYR R 635 " --> pdb=" O GLN R 631 " (cutoff:3.500A) Processing helix chain 'R' and resid 640 through 658 Processing helix chain 'R' and resid 660 through 677 removed outlier: 4.502A pdb=" N SER R 664 " --> pdb=" O ASN R 660 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN R 665 " --> pdb=" O THR R 661 " (cutoff:3.500A) Processing helix chain 'R' and resid 903 through 921 Processing helix chain 'R' and resid 922 through 936 removed outlier: 3.855A pdb=" N LEU R 926 " --> pdb=" O ASN R 922 " (cutoff:3.500A) Processing helix chain 'R' and resid 975 through 989 Processing helix chain 'R' and resid 990 through 1003 Processing helix chain 'R' and resid 1030 through 1046 Processing helix chain 'R' and resid 1164 through 1187 Processing helix chain 'R' and resid 1189 through 1207 removed outlier: 3.600A pdb=" N THR R1193 " --> pdb=" O ASN R1189 " (cutoff:3.500A) Processing helix chain 'R' and resid 1211 through 1233 Processing helix chain 'S' and resid 15 through 32 Processing helix chain 'S' and resid 32 through 45 removed outlier: 3.770A pdb=" N ILE S 36 " --> pdb=" O LEU S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 83 Proline residue: S 63 - end of helix Proline residue: S 74 - end of helix removed outlier: 3.665A pdb=" N ARG S 83 " --> pdb=" O TYR S 79 " (cutoff:3.500A) Processing helix chain 'T' and resid 16 through 45 Proline residue: T 34 - end of helix Processing helix chain 'T' and resid 53 through 82 Proline residue: T 63 - end of helix Proline residue: T 74 - end of helix Processing helix chain 'U' and resid 16 through 45 removed outlier: 3.637A pdb=" N PHE U 23 " --> pdb=" O LEU U 19 " (cutoff:3.500A) Proline residue: U 34 - end of helix Processing helix chain 'U' and resid 53 through 83 Proline residue: U 63 - end of helix Proline residue: U 74 - end of helix Processing helix chain 'V' and resid 3 through 20 Processing helix chain 'V' and resid 36 through 44 Processing helix chain 'V' and resid 60 through 96 Processing helix chain 'V' and resid 101 through 125 Processing helix chain 'W' and resid 136 through 159 Processing helix chain 'W' and resid 160 through 178 removed outlier: 3.824A pdb=" N ALA W 165 " --> pdb=" O PRO W 161 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE W 178 " --> pdb=" O ILE W 174 " (cutoff:3.500A) Processing helix chain 'W' and resid 184 through 204 removed outlier: 3.624A pdb=" N VAL W 188 " --> pdb=" O TYR W 184 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA W 194 " --> pdb=" O LEU W 190 " (cutoff:3.500A) Processing helix chain 'X' and resid 31 through 45 Processing helix chain 'X' and resid 67 through 79 Processing helix chain 'X' and resid 80 through 82 No H-bonds generated for 'chain 'X' and resid 80 through 82' Processing helix chain 'X' and resid 85 through 99 Processing helix chain 'X' and resid 598 through 612 removed outlier: 3.668A pdb=" N TYR X 612 " --> pdb=" O LEU X 608 " (cutoff:3.500A) Processing helix chain 'X' and resid 614 through 636 removed outlier: 3.560A pdb=" N TYR X 635 " --> pdb=" O GLN X 631 " (cutoff:3.500A) Processing helix chain 'X' and resid 640 through 658 Processing helix chain 'X' and resid 660 through 677 removed outlier: 4.502A pdb=" N SER X 664 " --> pdb=" O ASN X 660 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN X 665 " --> pdb=" O THR X 661 " (cutoff:3.500A) Processing helix chain 'X' and resid 903 through 921 Processing helix chain 'X' and resid 922 through 936 removed outlier: 3.854A pdb=" N LEU X 926 " --> pdb=" O ASN X 922 " (cutoff:3.500A) Processing helix chain 'X' and resid 975 through 989 Processing helix chain 'X' and resid 990 through 1003 Processing helix chain 'X' and resid 1030 through 1046 Processing helix chain 'X' and resid 1164 through 1187 Processing helix chain 'X' and resid 1189 through 1207 removed outlier: 3.601A pdb=" N THR X1193 " --> pdb=" O ASN X1189 " (cutoff:3.500A) Processing helix chain 'X' and resid 1211 through 1233 Processing helix chain 'Y' and resid 15 through 32 Processing helix chain 'Y' and resid 32 through 45 removed outlier: 3.769A pdb=" N ILE Y 36 " --> pdb=" O LEU Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 83 Proline residue: Y 63 - end of helix Proline residue: Y 74 - end of helix removed outlier: 3.664A pdb=" N ARG Y 83 " --> pdb=" O TYR Y 79 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 45 Proline residue: Z 34 - end of helix Processing helix chain 'Z' and resid 53 through 82 Proline residue: Z 63 - end of helix Proline residue: Z 74 - end of helix Processing helix chain '0' and resid 16 through 45 removed outlier: 3.638A pdb=" N PHE 0 23 " --> pdb=" O LEU 0 19 " (cutoff:3.500A) Proline residue: 0 34 - end of helix Processing helix chain '0' and resid 53 through 83 Proline residue: 0 63 - end of helix Proline residue: 0 74 - end of helix Processing helix chain '1' and resid 3 through 20 Processing helix chain '1' and resid 36 through 44 Processing helix chain '1' and resid 60 through 96 Processing helix chain '1' and resid 101 through 125 Processing helix chain '2' and resid 136 through 159 Processing helix chain '2' and resid 160 through 178 removed outlier: 3.825A pdb=" N ALA 2 165 " --> pdb=" O PRO 2 161 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE 2 178 " --> pdb=" O ILE 2 174 " (cutoff:3.500A) Processing helix chain '2' and resid 184 through 204 removed outlier: 3.625A pdb=" N VAL 2 188 " --> pdb=" O TYR 2 184 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA 2 194 " --> pdb=" O LEU 2 190 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 45 Processing helix chain '3' and resid 67 through 79 Processing helix chain '3' and resid 80 through 82 No H-bonds generated for 'chain '3' and resid 80 through 82' Processing helix chain '3' and resid 85 through 99 Processing helix chain '3' and resid 598 through 612 removed outlier: 3.668A pdb=" N TYR 3 612 " --> pdb=" O LEU 3 608 " (cutoff:3.500A) Processing helix chain '3' and resid 614 through 636 removed outlier: 3.560A pdb=" N TYR 3 635 " --> pdb=" O GLN 3 631 " (cutoff:3.500A) Processing helix chain '3' and resid 640 through 658 Processing helix chain '3' and resid 660 through 677 removed outlier: 4.502A pdb=" N SER 3 664 " --> pdb=" O ASN 3 660 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN 3 665 " --> pdb=" O THR 3 661 " (cutoff:3.500A) Processing helix chain '3' and resid 903 through 921 Processing helix chain '3' and resid 922 through 936 removed outlier: 3.855A pdb=" N LEU 3 926 " --> pdb=" O ASN 3 922 " (cutoff:3.500A) Processing helix chain '3' and resid 975 through 989 Processing helix chain '3' and resid 990 through 1003 Processing helix chain '3' and resid 1030 through 1046 Processing helix chain '3' and resid 1164 through 1187 Processing helix chain '3' and resid 1189 through 1207 removed outlier: 3.600A pdb=" N THR 31193 " --> pdb=" O ASN 31189 " (cutoff:3.500A) Processing helix chain '3' and resid 1211 through 1233 Processing helix chain '4' and resid 15 through 32 Processing helix chain '4' and resid 32 through 45 removed outlier: 3.770A pdb=" N ILE 4 36 " --> pdb=" O LEU 4 32 " (cutoff:3.500A) Processing helix chain '4' and resid 52 through 83 Proline residue: 4 63 - end of helix Proline residue: 4 74 - end of helix removed outlier: 3.665A pdb=" N ARG 4 83 " --> pdb=" O TYR 4 79 " (cutoff:3.500A) Processing helix chain '5' and resid 16 through 45 Proline residue: 5 34 - end of helix Processing helix chain '5' and resid 53 through 82 Proline residue: 5 63 - end of helix Proline residue: 5 74 - end of helix Processing helix chain '6' and resid 16 through 45 removed outlier: 3.637A pdb=" N PHE 6 23 " --> pdb=" O LEU 6 19 " (cutoff:3.500A) Proline residue: 6 34 - end of helix Processing helix chain '6' and resid 53 through 83 Proline residue: 6 63 - end of helix Proline residue: 6 74 - end of helix Processing helix chain '7' and resid 3 through 20 Processing helix chain '7' and resid 36 through 44 Processing helix chain '7' and resid 60 through 96 Processing helix chain '7' and resid 101 through 125 Processing helix chain '8' and resid 136 through 159 Processing helix chain '8' and resid 160 through 178 removed outlier: 3.825A pdb=" N ALA 8 165 " --> pdb=" O PRO 8 161 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE 8 178 " --> pdb=" O ILE 8 174 " (cutoff:3.500A) Processing helix chain '8' and resid 184 through 204 removed outlier: 3.624A pdb=" N VAL 8 188 " --> pdb=" O TYR 8 184 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA 8 194 " --> pdb=" O LEU 8 190 " (cutoff:3.500A) Processing helix chain '9' and resid 31 through 45 Processing helix chain '9' and resid 67 through 79 Processing helix chain '9' and resid 80 through 82 No H-bonds generated for 'chain '9' and resid 80 through 82' Processing helix chain '9' and resid 85 through 99 Processing helix chain '9' and resid 598 through 612 removed outlier: 3.668A pdb=" N TYR 9 612 " --> pdb=" O LEU 9 608 " (cutoff:3.500A) Processing helix chain '9' and resid 614 through 636 removed outlier: 3.559A pdb=" N TYR 9 635 " --> pdb=" O GLN 9 631 " (cutoff:3.500A) Processing helix chain '9' and resid 640 through 658 Processing helix chain '9' and resid 660 through 677 removed outlier: 4.502A pdb=" N SER 9 664 " --> pdb=" O ASN 9 660 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN 9 665 " --> pdb=" O THR 9 661 " (cutoff:3.500A) Processing helix chain '9' and resid 903 through 921 Processing helix chain '9' and resid 922 through 936 removed outlier: 3.855A pdb=" N LEU 9 926 " --> pdb=" O ASN 9 922 " (cutoff:3.500A) Processing helix chain '9' and resid 975 through 989 Processing helix chain '9' and resid 990 through 1003 Processing helix chain '9' and resid 1030 through 1046 Processing helix chain '9' and resid 1164 through 1187 Processing helix chain '9' and resid 1189 through 1207 removed outlier: 3.600A pdb=" N THR 91193 " --> pdb=" O ASN 91189 " (cutoff:3.500A) Processing helix chain '9' and resid 1211 through 1233 Processing helix chain 'a' and resid 15 through 32 Processing helix chain 'a' and resid 32 through 45 removed outlier: 3.769A pdb=" N ILE a 36 " --> pdb=" O LEU a 32 " (cutoff:3.500A) Processing helix chain 'a' and resid 52 through 83 Proline residue: a 63 - end of helix Proline residue: a 74 - end of helix removed outlier: 3.664A pdb=" N ARG a 83 " --> pdb=" O TYR a 79 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 45 Proline residue: b 34 - end of helix Processing helix chain 'b' and resid 53 through 82 Proline residue: b 63 - end of helix Proline residue: b 74 - end of helix Processing helix chain 'c' and resid 16 through 45 removed outlier: 3.638A pdb=" N PHE c 23 " --> pdb=" O LEU c 19 " (cutoff:3.500A) Proline residue: c 34 - end of helix Processing helix chain 'c' and resid 53 through 83 Proline residue: c 63 - end of helix Proline residue: c 74 - end of helix Processing helix chain 'd' and resid 3 through 20 Processing helix chain 'd' and resid 36 through 44 Processing helix chain 'd' and resid 60 through 96 Processing helix chain 'd' and resid 101 through 125 Processing helix chain 'e' and resid 136 through 159 Processing helix chain 'e' and resid 160 through 178 removed outlier: 3.825A pdb=" N ALA e 165 " --> pdb=" O PRO e 161 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE e 178 " --> pdb=" O ILE e 174 " (cutoff:3.500A) Processing helix chain 'e' and resid 184 through 204 removed outlier: 3.625A pdb=" N VAL e 188 " --> pdb=" O TYR e 184 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA e 194 " --> pdb=" O LEU e 190 " (cutoff:3.500A) Processing helix chain 'f' and resid 31 through 45 Processing helix chain 'f' and resid 67 through 79 Processing helix chain 'f' and resid 80 through 82 No H-bonds generated for 'chain 'f' and resid 80 through 82' Processing helix chain 'f' and resid 85 through 99 Processing helix chain 'f' and resid 598 through 612 removed outlier: 3.669A pdb=" N TYR f 612 " --> pdb=" O LEU f 608 " (cutoff:3.500A) Processing helix chain 'f' and resid 614 through 636 removed outlier: 3.559A pdb=" N TYR f 635 " --> pdb=" O GLN f 631 " (cutoff:3.500A) Processing helix chain 'f' and resid 640 through 658 Processing helix chain 'f' and resid 660 through 677 removed outlier: 4.501A pdb=" N SER f 664 " --> pdb=" O ASN f 660 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN f 665 " --> pdb=" O THR f 661 " (cutoff:3.500A) Processing helix chain 'f' and resid 903 through 921 Processing helix chain 'f' and resid 922 through 936 removed outlier: 3.855A pdb=" N LEU f 926 " --> pdb=" O ASN f 922 " (cutoff:3.500A) Processing helix chain 'f' and resid 975 through 989 Processing helix chain 'f' and resid 990 through 1003 Processing helix chain 'f' and resid 1030 through 1046 Processing helix chain 'f' and resid 1164 through 1187 Processing helix chain 'f' and resid 1189 through 1207 removed outlier: 3.600A pdb=" N THR f1193 " --> pdb=" O ASN f1189 " (cutoff:3.500A) Processing helix chain 'f' and resid 1211 through 1233 Processing sheet with id= 1, first strand: chain 'D' and resid 47 through 50 Processing sheet with id= 2, first strand: chain 'E' and resid 25 through 27 Processing sheet with id= 3, first strand: chain 'E' and resid 69 through 75 removed outlier: 4.641A pdb=" N GLU E 73 " --> pdb=" O TYR E 57 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR E 57 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'E' and resid 120 through 124 Processing sheet with id= 5, first strand: chain 'F' and resid 47 through 48 Processing sheet with id= 6, first strand: chain 'F' and resid 1005 through 1007 Processing sheet with id= 7, first strand: chain 'F' and resid 1051 through 1056 removed outlier: 7.231A pdb=" N ILE F1088 " --> pdb=" O PHE F1053 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA F1055 " --> pdb=" O GLN F1086 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN F1086 " --> pdb=" O ALA F1055 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'F' and resid 1062 through 1069 removed outlier: 4.959A pdb=" N ILE F1063 " --> pdb=" O TYR F1078 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR F1078 " --> pdb=" O ILE F1063 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'J' and resid 47 through 50 Processing sheet with id= 10, first strand: chain 'K' and resid 25 through 27 Processing sheet with id= 11, first strand: chain 'K' and resid 69 through 75 removed outlier: 4.640A pdb=" N GLU K 73 " --> pdb=" O TYR K 57 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR K 57 " --> pdb=" O GLU K 73 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'K' and resid 120 through 124 Processing sheet with id= 13, first strand: chain 'L' and resid 47 through 48 Processing sheet with id= 14, first strand: chain 'L' and resid 1005 through 1007 Processing sheet with id= 15, first strand: chain 'L' and resid 1051 through 1056 removed outlier: 7.231A pdb=" N ILE L1088 " --> pdb=" O PHE L1053 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA L1055 " --> pdb=" O GLN L1086 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN L1086 " --> pdb=" O ALA L1055 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'L' and resid 1062 through 1069 removed outlier: 4.959A pdb=" N ILE L1063 " --> pdb=" O TYR L1078 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR L1078 " --> pdb=" O ILE L1063 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'P' and resid 47 through 50 Processing sheet with id= 18, first strand: chain 'Q' and resid 25 through 27 Processing sheet with id= 19, first strand: chain 'Q' and resid 69 through 75 removed outlier: 4.640A pdb=" N GLU Q 73 " --> pdb=" O TYR Q 57 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR Q 57 " --> pdb=" O GLU Q 73 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'Q' and resid 120 through 124 Processing sheet with id= 21, first strand: chain 'R' and resid 47 through 48 Processing sheet with id= 22, first strand: chain 'R' and resid 1005 through 1007 Processing sheet with id= 23, first strand: chain 'R' and resid 1051 through 1056 removed outlier: 7.231A pdb=" N ILE R1088 " --> pdb=" O PHE R1053 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA R1055 " --> pdb=" O GLN R1086 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN R1086 " --> pdb=" O ALA R1055 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'R' and resid 1062 through 1069 removed outlier: 4.959A pdb=" N ILE R1063 " --> pdb=" O TYR R1078 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR R1078 " --> pdb=" O ILE R1063 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'V' and resid 47 through 50 Processing sheet with id= 26, first strand: chain 'W' and resid 25 through 27 Processing sheet with id= 27, first strand: chain 'W' and resid 69 through 75 removed outlier: 4.641A pdb=" N GLU W 73 " --> pdb=" O TYR W 57 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR W 57 " --> pdb=" O GLU W 73 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'W' and resid 120 through 124 Processing sheet with id= 29, first strand: chain 'X' and resid 47 through 48 Processing sheet with id= 30, first strand: chain 'X' and resid 1005 through 1007 Processing sheet with id= 31, first strand: chain 'X' and resid 1051 through 1056 removed outlier: 7.232A pdb=" N ILE X1088 " --> pdb=" O PHE X1053 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA X1055 " --> pdb=" O GLN X1086 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN X1086 " --> pdb=" O ALA X1055 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'X' and resid 1062 through 1069 removed outlier: 4.960A pdb=" N ILE X1063 " --> pdb=" O TYR X1078 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR X1078 " --> pdb=" O ILE X1063 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain '1' and resid 47 through 50 Processing sheet with id= 34, first strand: chain '2' and resid 25 through 27 Processing sheet with id= 35, first strand: chain '2' and resid 69 through 75 removed outlier: 4.641A pdb=" N GLU 2 73 " --> pdb=" O TYR 2 57 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR 2 57 " --> pdb=" O GLU 2 73 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain '2' and resid 120 through 124 Processing sheet with id= 37, first strand: chain '3' and resid 47 through 48 Processing sheet with id= 38, first strand: chain '3' and resid 1005 through 1007 Processing sheet with id= 39, first strand: chain '3' and resid 1051 through 1056 removed outlier: 7.230A pdb=" N ILE 31088 " --> pdb=" O PHE 31053 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA 31055 " --> pdb=" O GLN 31086 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN 31086 " --> pdb=" O ALA 31055 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain '3' and resid 1062 through 1069 removed outlier: 4.959A pdb=" N ILE 31063 " --> pdb=" O TYR 31078 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR 31078 " --> pdb=" O ILE 31063 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain '7' and resid 47 through 50 Processing sheet with id= 42, first strand: chain '8' and resid 25 through 27 Processing sheet with id= 43, first strand: chain '8' and resid 69 through 75 removed outlier: 4.641A pdb=" N GLU 8 73 " --> pdb=" O TYR 8 57 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR 8 57 " --> pdb=" O GLU 8 73 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain '8' and resid 120 through 124 Processing sheet with id= 45, first strand: chain '9' and resid 47 through 48 Processing sheet with id= 46, first strand: chain '9' and resid 1005 through 1007 Processing sheet with id= 47, first strand: chain '9' and resid 1051 through 1056 removed outlier: 7.231A pdb=" N ILE 91088 " --> pdb=" O PHE 91053 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA 91055 " --> pdb=" O GLN 91086 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN 91086 " --> pdb=" O ALA 91055 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain '9' and resid 1062 through 1069 removed outlier: 4.959A pdb=" N ILE 91063 " --> pdb=" O TYR 91078 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR 91078 " --> pdb=" O ILE 91063 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'd' and resid 47 through 50 Processing sheet with id= 50, first strand: chain 'e' and resid 25 through 27 Processing sheet with id= 51, first strand: chain 'e' and resid 69 through 75 removed outlier: 4.642A pdb=" N GLU e 73 " --> pdb=" O TYR e 57 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR e 57 " --> pdb=" O GLU e 73 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'e' and resid 120 through 124 Processing sheet with id= 53, first strand: chain 'f' and resid 47 through 48 Processing sheet with id= 54, first strand: chain 'f' and resid 1005 through 1007 Processing sheet with id= 55, first strand: chain 'f' and resid 1051 through 1056 removed outlier: 7.231A pdb=" N ILE f1088 " --> pdb=" O PHE f1053 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA f1055 " --> pdb=" O GLN f1086 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN f1086 " --> pdb=" O ALA f1055 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'f' and resid 1062 through 1069 removed outlier: 4.959A pdb=" N ILE f1063 " --> pdb=" O TYR f1078 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR f1078 " --> pdb=" O ILE f1063 " (cutoff:3.500A) 3570 hydrogen bonds defined for protein. 10542 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: 15.73 Time building geometry restraints manager: 18.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15922 1.34 - 1.46: 13486 1.46 - 1.58: 25409 1.58 - 1.70: 0 1.70 - 1.81: 336 Bond restraints: 55153 Sorted by residual: bond pdb=" CB PRO K 49 " pdb=" CG PRO K 49 " ideal model delta sigma weight residual 1.492 1.575 -0.083 5.00e-02 4.00e+02 2.76e+00 bond pdb=" CB PRO Q 49 " pdb=" CG PRO Q 49 " ideal model delta sigma weight residual 1.492 1.575 -0.083 5.00e-02 4.00e+02 2.74e+00 bond pdb=" CB PRO 8 49 " pdb=" CG PRO 8 49 " ideal model delta sigma weight residual 1.492 1.575 -0.083 5.00e-02 4.00e+02 2.73e+00 bond pdb=" CB PRO E 49 " pdb=" CG PRO E 49 " ideal model delta sigma weight residual 1.492 1.574 -0.082 5.00e-02 4.00e+02 2.72e+00 bond pdb=" CB PRO 2 49 " pdb=" CG PRO 2 49 " ideal model delta sigma weight residual 1.492 1.574 -0.082 5.00e-02 4.00e+02 2.70e+00 ... (remaining 55148 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.52: 1669 106.52 - 113.44: 30334 113.44 - 120.36: 20682 120.36 - 127.28: 22329 127.28 - 134.20: 677 Bond angle restraints: 75691 Sorted by residual: angle pdb=" C VAL e 101 " pdb=" N ASN e 102 " pdb=" CA ASN e 102 " ideal model delta sigma weight residual 121.54 129.69 -8.15 1.91e+00 2.74e-01 1.82e+01 angle pdb=" C VAL K 101 " pdb=" N ASN K 102 " pdb=" CA ASN K 102 " ideal model delta sigma weight residual 121.54 129.68 -8.14 1.91e+00 2.74e-01 1.82e+01 angle pdb=" C VAL W 101 " pdb=" N ASN W 102 " pdb=" CA ASN W 102 " ideal model delta sigma weight residual 121.54 129.68 -8.14 1.91e+00 2.74e-01 1.82e+01 angle pdb=" C VAL 2 101 " pdb=" N ASN 2 102 " pdb=" CA ASN 2 102 " ideal model delta sigma weight residual 121.54 129.68 -8.14 1.91e+00 2.74e-01 1.82e+01 angle pdb=" C VAL E 101 " pdb=" N ASN E 102 " pdb=" CA ASN E 102 " ideal model delta sigma weight residual 121.54 129.68 -8.14 1.91e+00 2.74e-01 1.81e+01 ... (remaining 75686 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 27152 17.99 - 35.98: 3445 35.98 - 53.97: 882 53.97 - 71.96: 91 71.96 - 89.95: 42 Dihedral angle restraints: 31612 sinusoidal: 11641 harmonic: 19971 Sorted by residual: dihedral pdb=" CA PRO 2 49 " pdb=" C PRO 2 49 " pdb=" N THR 2 50 " pdb=" CA THR 2 50 " ideal model delta harmonic sigma weight residual 180.00 157.57 22.43 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PRO e 49 " pdb=" C PRO e 49 " pdb=" N THR e 50 " pdb=" CA THR e 50 " ideal model delta harmonic sigma weight residual 180.00 157.57 22.43 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PRO E 49 " pdb=" C PRO E 49 " pdb=" N THR E 50 " pdb=" CA THR E 50 " ideal model delta harmonic sigma weight residual 180.00 157.58 22.42 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 31609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 7256 0.054 - 0.107: 1554 0.107 - 0.161: 191 0.161 - 0.215: 22 0.215 - 0.269: 7 Chirality restraints: 9030 Sorted by residual: chirality pdb=" CG LEU S 59 " pdb=" CB LEU S 59 " pdb=" CD1 LEU S 59 " pdb=" CD2 LEU S 59 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CG LEU A 59 " pdb=" CB LEU A 59 " pdb=" CD1 LEU A 59 " pdb=" CD2 LEU A 59 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CG LEU G 59 " pdb=" CB LEU G 59 " pdb=" CD1 LEU G 59 " pdb=" CD2 LEU G 59 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 9027 not shown) Planarity restraints: 9247 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU Q 48 " -0.077 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO Q 49 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO Q 49 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO Q 49 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU 8 48 " 0.076 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO 8 49 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO 8 49 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO 8 49 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU K 48 " -0.076 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO K 49 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO K 49 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO K 49 " -0.062 5.00e-02 4.00e+02 ... (remaining 9244 not shown) Histogram of nonbonded interaction distances: 0.14 - 1.09: 98 1.09 - 2.04: 392 2.04 - 2.99: 31344 2.99 - 3.95: 148308 3.95 - 4.90: 260987 Warning: very small nonbonded interaction distances. Nonbonded interactions: 441129 Sorted by model distance: nonbonded pdb=" CE MET X1214 " pdb=" CG PHE 2 173 " model vdw 0.137 3.680 nonbonded pdb=" CE MET 91214 " pdb=" CG PHE e 173 " model vdw 0.137 3.680 nonbonded pdb=" CE MET 31214 " pdb=" CG PHE 8 173 " model vdw 0.137 3.680 nonbonded pdb=" CE MET R1214 " pdb=" CG PHE W 173 " model vdw 0.137 3.680 nonbonded pdb=" CE MET F1214 " pdb=" CG PHE K 173 " model vdw 0.137 3.680 ... (remaining 441124 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 '0' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain '1' selection = chain '7' selection = chain 'D' selection = chain 'J' selection = chain 'P' selection = chain 'V' selection = chain 'd' } ncs_group { reference = chain '2' selection = chain '8' selection = chain 'E' selection = chain 'K' selection = chain 'Q' selection = chain 'W' selection = chain 'e' } ncs_group { reference = chain '3' selection = chain '9' selection = chain 'F' selection = chain 'L' selection = chain 'R' selection = chain 'X' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 16.420 Check model and map are aligned: 0.600 Set scattering table: 0.380 Process input model: 97.280 Find NCS groups from input model: 2.770 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 0.083 55153 Z= 0.220 Angle : 0.711 12.554 75691 Z= 0.351 Chirality : 0.043 0.269 9030 Planarity : 0.006 0.115 9247 Dihedral : 16.854 89.953 18788 Min Nonbonded Distance : 0.137 Molprobity Statistics. All-atom Clashscore : 25.89 Ramachandran Plot: Outliers : 0.63 % Allowed : 4.73 % Favored : 94.64 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.10), residues: 6664 helix: 1.50 (0.08), residues: 4116 sheet: -0.23 (0.20), residues: 609 loop : -2.21 (0.13), residues: 1939 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1491 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1458 time to evaluate : 5.246 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 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 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 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: 33 outliers final: 15 residues processed: 1473 average time/residue: 0.4592 time to fit residues: 1186.5653 Evaluate side-chains 1331 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1316 time to evaluate : 4.453 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3786 time to fit residues: 16.8170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 549 optimal weight: 0.4980 chunk 493 optimal weight: 1.9990 chunk 273 optimal weight: 0.6980 chunk 168 optimal weight: 0.8980 chunk 332 optimal weight: 2.9990 chunk 263 optimal weight: 5.9990 chunk 510 optimal weight: 0.4980 chunk 197 optimal weight: 3.9990 chunk 310 optimal weight: 0.0170 chunk 379 optimal weight: 5.9990 chunk 591 optimal weight: 0.2980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 33 ASN D 39 GLN D 43 GLN ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1166 ASN J 43 GLN K 113 GLN ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1166 ASN ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 GLN R 57 HIS ** R 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R1166 ASN X 57 HIS ** X 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1166 ASN 2 113 GLN ** 3 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 31043 ASN ** 31136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 31166 ASN 4 60 ASN 8 34 ASN 9 64 ASN ** 9 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 91136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 91166 ASN d 39 GLN f 64 ASN ** f 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f1166 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 55153 Z= 0.247 Angle : 0.734 12.971 75691 Z= 0.367 Chirality : 0.045 0.361 9030 Planarity : 0.006 0.114 9247 Dihedral : 4.816 22.753 7245 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.63 % Allowed : 5.04 % Favored : 94.33 % Rotamer Outliers : 5.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.10), residues: 6664 helix: 1.52 (0.08), residues: 4109 sheet: -0.28 (0.20), residues: 609 loop : -2.15 (0.13), residues: 1946 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1753 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 320 poor density : 1433 time to evaluate : 4.481 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 320 outliers final: 190 residues processed: 1608 average time/residue: 0.4627 time to fit residues: 1301.1893 Evaluate side-chains 1500 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1310 time to evaluate : 4.419 Switching outliers to nearest non-outliers outliers start: 190 outliers final: 0 residues processed: 190 average time/residue: 0.4001 time to fit residues: 149.7081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 328 optimal weight: 0.0370 chunk 183 optimal weight: 0.9980 chunk 492 optimal weight: 0.9980 chunk 402 optimal weight: 0.6980 chunk 163 optimal weight: 6.9990 chunk 592 optimal weight: 0.7980 chunk 639 optimal weight: 0.9980 chunk 527 optimal weight: 0.9980 chunk 587 optimal weight: 0.5980 chunk 201 optimal weight: 5.9990 chunk 475 optimal weight: 0.0170 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN D 43 GLN ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 43 GLN K 34 ASN L 64 ASN ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 GLN ** L 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 GLN R 71 ASN ** R 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 GLN ** X 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 98 GLN ** 3 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 64 ASN ** 9 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 669 GLN 91135 ASN ** 91136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 GLN f 64 ASN ** f 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 97 GLN f 98 GLN ** f 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.081 55153 Z= 0.222 Angle : 0.696 10.450 75691 Z= 0.346 Chirality : 0.045 0.435 9030 Planarity : 0.006 0.112 9247 Dihedral : 4.780 24.523 7245 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.63 % Allowed : 4.86 % Favored : 94.51 % Rotamer Outliers : 3.17 % 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: 0.62 (0.10), residues: 6664 helix: 1.62 (0.08), residues: 4130 sheet: -0.24 (0.20), residues: 595 loop : -2.12 (0.13), residues: 1939 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1605 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1419 time to evaluate : 4.551 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 revert: symmetry clash outliers start: 186 outliers final: 82 residues processed: 1532 average time/residue: 0.4721 time to fit residues: 1260.5308 Evaluate side-chains 1389 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1307 time to evaluate : 4.402 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 0 residues processed: 82 average time/residue: 0.3837 time to fit residues: 65.4073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 585 optimal weight: 0.2980 chunk 445 optimal weight: 0.2980 chunk 307 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 282 optimal weight: 50.0000 chunk 397 optimal weight: 0.6980 chunk 594 optimal weight: 0.9980 chunk 629 optimal weight: 6.9990 chunk 310 optimal weight: 0.9980 chunk 563 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN D 43 GLN ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1135 ASN J 39 GLN K 55 GLN L 64 ASN ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 GLN ** L 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 669 GLN P 39 GLN Q 55 GLN ** R 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 55 GLN ** X 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 98 GLN ** 3 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 64 ASN ** 9 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 91135 ASN 91166 ASN d 39 GLN f 64 ASN ** f 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 55153 Z= 0.224 Angle : 0.686 13.747 75691 Z= 0.340 Chirality : 0.044 0.392 9030 Planarity : 0.005 0.112 9247 Dihedral : 4.737 24.837 7245 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.63 % Allowed : 4.95 % Favored : 94.42 % Rotamer Outliers : 4.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.10), residues: 6664 helix: 1.74 (0.08), residues: 4102 sheet: -0.20 (0.20), residues: 595 loop : -2.11 (0.13), residues: 1967 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1646 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 1382 time to evaluate : 4.494 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: 264 outliers final: 138 residues processed: 1520 average time/residue: 0.4840 time to fit residues: 1263.7032 Evaluate side-chains 1430 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1292 time to evaluate : 4.457 Switching outliers to nearest non-outliers outliers start: 138 outliers final: 0 residues processed: 138 average time/residue: 0.4060 time to fit residues: 108.9285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 524 optimal weight: 2.9990 chunk 357 optimal weight: 1.9990 chunk 9 optimal weight: 30.0000 chunk 468 optimal weight: 40.0000 chunk 259 optimal weight: 0.8980 chunk 536 optimal weight: 5.9990 chunk 434 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 321 optimal weight: 0.9990 chunk 564 optimal weight: 0.2980 chunk 158 optimal weight: 10.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN D 43 GLN D 49 ASN ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1135 ASN J 39 GLN L 64 ASN ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 596 ASN P 49 ASN ** R 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 GLN X 596 ASN X1043 ASN ** X1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 596 ASN ** 3 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 49 ASN 9 64 ASN ** 9 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 98 GLN ** 9 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 91135 ASN d 39 GLN e 55 GLN f 64 ASN ** f 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 55153 Z= 0.303 Angle : 0.715 15.968 75691 Z= 0.356 Chirality : 0.044 0.329 9030 Planarity : 0.006 0.114 9247 Dihedral : 4.756 24.443 7245 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.65 % Allowed : 5.15 % Favored : 94.21 % Rotamer Outliers : 3.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.10), residues: 6664 helix: 1.74 (0.08), residues: 4102 sheet: -0.25 (0.20), residues: 609 loop : -2.12 (0.13), residues: 1953 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1622 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1388 time to evaluate : 4.498 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: 234 outliers final: 130 residues processed: 1499 average time/residue: 0.4716 time to fit residues: 1237.3205 Evaluate side-chains 1448 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1318 time to evaluate : 4.444 Switching outliers to nearest non-outliers outliers start: 130 outliers final: 0 residues processed: 130 average time/residue: 0.3874 time to fit residues: 101.3913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 211 optimal weight: 0.7980 chunk 566 optimal weight: 10.0000 chunk 124 optimal weight: 0.0370 chunk 369 optimal weight: 0.5980 chunk 155 optimal weight: 5.9990 chunk 629 optimal weight: 0.8980 chunk 522 optimal weight: 6.9990 chunk 291 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 208 optimal weight: 1.9990 chunk 330 optimal weight: 4.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN D 43 GLN E 55 GLN ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1135 ASN J 39 GLN J 113 ASN L 64 ASN ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 49 ASN ** R 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 596 ASN ** V 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1043 ASN ** 3 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 49 ASN 8 55 GLN 9 63 ASN 9 64 ASN ** 9 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 91135 ASN d 39 GLN f 57 HIS ** f 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f1135 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 55153 Z= 0.221 Angle : 0.716 16.160 75691 Z= 0.348 Chirality : 0.044 0.294 9030 Planarity : 0.006 0.170 9247 Dihedral : 4.770 31.189 7245 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.65 % Allowed : 5.09 % Favored : 94.27 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.28 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.10), residues: 6664 helix: 1.78 (0.08), residues: 4095 sheet: 0.07 (0.22), residues: 511 loop : -2.10 (0.13), residues: 2058 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1552 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1373 time to evaluate : 4.450 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 179 outliers final: 97 residues processed: 1467 average time/residue: 0.4888 time to fit residues: 1254.7855 Evaluate side-chains 1388 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1291 time to evaluate : 4.457 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 0 residues processed: 97 average time/residue: 0.4200 time to fit residues: 80.7840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 607 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 358 optimal weight: 2.9990 chunk 459 optimal weight: 0.6980 chunk 356 optimal weight: 0.9980 chunk 530 optimal weight: 3.9990 chunk 351 optimal weight: 0.9990 chunk 627 optimal weight: 3.9990 chunk 392 optimal weight: 2.9990 chunk 382 optimal weight: 0.9980 chunk 289 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN D 43 GLN ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1135 ASN J 39 GLN ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN L 64 ASN ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 669 GLN P 113 ASN ** R 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 GLN ** V 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 GLN ** X 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1043 ASN ** X1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 113 ASN ** 3 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 49 ASN 8 52 ASN 9 64 ASN ** 9 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 91135 ASN d 39 GLN ** f 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 55153 Z= 0.249 Angle : 0.729 15.765 75691 Z= 0.354 Chirality : 0.044 0.320 9030 Planarity : 0.006 0.141 9247 Dihedral : 4.777 31.039 7245 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.65 % Allowed : 5.21 % Favored : 94.15 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.28 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.10), residues: 6664 helix: 1.72 (0.08), residues: 4088 sheet: 0.06 (0.22), residues: 511 loop : -2.10 (0.13), residues: 2065 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1451 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1316 time to evaluate : 4.460 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: 135 outliers final: 62 residues processed: 1390 average time/residue: 0.4690 time to fit residues: 1137.0597 Evaluate side-chains 1329 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1267 time to evaluate : 4.454 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 0.4064 time to fit residues: 52.4765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 388 optimal weight: 0.0000 chunk 250 optimal weight: 5.9990 chunk 374 optimal weight: 2.9990 chunk 189 optimal weight: 40.0000 chunk 123 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 398 optimal weight: 0.5980 chunk 427 optimal weight: 0.6980 chunk 310 optimal weight: 0.0070 chunk 58 optimal weight: 5.9990 chunk 493 optimal weight: 0.7980 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN D 43 GLN ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1135 ASN J 39 GLN K 113 GLN L 64 ASN ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 669 GLN L1043 ASN ** R 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 GLN X 596 ASN ** X 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 669 GLN 7 49 ASN 7 113 ASN ** 8 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 64 ASN ** 9 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 91135 ASN d 39 GLN d 113 ASN ** f 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 991 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 55153 Z= 0.215 Angle : 0.732 18.698 75691 Z= 0.353 Chirality : 0.044 0.283 9030 Planarity : 0.006 0.127 9247 Dihedral : 4.769 31.372 7245 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.63 % Allowed : 5.21 % Favored : 94.16 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.28 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.10), residues: 6664 helix: 1.74 (0.08), residues: 4081 sheet: 0.10 (0.22), residues: 511 loop : -2.11 (0.13), residues: 2072 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1440 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1329 time to evaluate : 4.647 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: 111 outliers final: 56 residues processed: 1386 average time/residue: 0.4703 time to fit residues: 1137.0216 Evaluate side-chains 1308 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1252 time to evaluate : 4.461 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.3975 time to fit residues: 47.6521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 570 optimal weight: 0.0070 chunk 601 optimal weight: 0.9980 chunk 548 optimal weight: 3.9990 chunk 584 optimal weight: 0.9980 chunk 600 optimal weight: 0.7980 chunk 351 optimal weight: 0.9990 chunk 254 optimal weight: 0.9980 chunk 459 optimal weight: 0.8980 chunk 179 optimal weight: 5.9990 chunk 528 optimal weight: 0.8980 chunk 553 optimal weight: 0.6980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN D 43 GLN ** F 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1135 ASN J 39 GLN L 57 HIS L 64 ASN ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 669 GLN L 991 ASN ** R 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 GLN ** X 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 49 ASN ** 8 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 57 HIS 9 64 ASN ** 9 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 GLN d 113 ASN ** f 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 55153 Z= 0.229 Angle : 0.748 25.619 75691 Z= 0.358 Chirality : 0.044 0.350 9030 Planarity : 0.006 0.197 9247 Dihedral : 4.782 33.635 7245 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.63 % Allowed : 5.16 % Favored : 94.21 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.10), residues: 6664 helix: 1.71 (0.08), residues: 4088 sheet: 0.08 (0.22), residues: 511 loop : -2.15 (0.13), residues: 2065 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1389 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1314 time to evaluate : 4.487 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 outliers start: 75 outliers final: 43 residues processed: 1351 average time/residue: 0.4944 time to fit residues: 1168.0766 Evaluate side-chains 1303 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1260 time to evaluate : 4.435 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.4158 time to fit residues: 38.8233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 582 optimal weight: 0.9980 chunk 383 optimal weight: 7.9990 chunk 618 optimal weight: 2.9990 chunk 377 optimal weight: 3.9990 chunk 293 optimal weight: 0.9990 chunk 429 optimal weight: 0.4980 chunk 648 optimal weight: 0.7980 chunk 596 optimal weight: 1.9990 chunk 516 optimal weight: 2.9990 chunk 53 optimal weight: 0.0970 chunk 398 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN D 43 GLN ** F 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1135 ASN J 39 GLN L 64 ASN ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 669 GLN ** R 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 GLN ** X 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 49 ASN ** 8 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 57 HIS 9 64 ASN ** 9 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 91136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 GLN ** f 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 55153 Z= 0.230 Angle : 0.761 25.568 75691 Z= 0.361 Chirality : 0.045 0.361 9030 Planarity : 0.006 0.198 9247 Dihedral : 4.795 38.303 7245 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.65 % Allowed : 5.30 % Favored : 94.06 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.10), residues: 6664 helix: 1.72 (0.08), residues: 4074 sheet: 0.08 (0.22), residues: 511 loop : -2.14 (0.12), residues: 2079 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1325 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1286 time to evaluate : 4.856 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 outliers start: 39 outliers final: 21 residues processed: 1303 average time/residue: 0.4737 time to fit residues: 1074.7766 Evaluate side-chains 1269 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1248 time to evaluate : 4.482 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.4146 time to fit residues: 21.9478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 316 optimal weight: 1.9990 chunk 410 optimal weight: 0.9990 chunk 550 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 476 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 143 optimal weight: 0.9990 chunk 517 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 531 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN D 43 GLN ** F 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1135 ASN J 39 GLN L 64 ASN ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 669 GLN ** R 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1135 ASN ** S 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 49 ASN ** 8 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 64 ASN ** 9 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 GLN ** f 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.136979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.107522 restraints weight = 81336.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.109918 restraints weight = 45807.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.111414 restraints weight = 30844.077| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 55153 Z= 0.247 Angle : 0.769 27.075 75691 Z= 0.365 Chirality : 0.045 0.341 9030 Planarity : 0.006 0.202 9247 Dihedral : 4.828 39.958 7245 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.63 % Allowed : 5.33 % Favored : 94.04 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.10), residues: 6664 helix: 1.70 (0.08), residues: 4102 sheet: 0.05 (0.22), residues: 511 loop : -2.16 (0.13), residues: 2051 =============================================================================== Job complete usr+sys time: 16219.66 seconds wall clock time: 282 minutes 51.93 seconds (16971.93 seconds total)