Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 05:12:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5i_22681/04_2023/7k5i_22681.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5i_22681/04_2023/7k5i_22681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5i_22681/04_2023/7k5i_22681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5i_22681/04_2023/7k5i_22681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5i_22681/04_2023/7k5i_22681.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5i_22681/04_2023/7k5i_22681.pdb" } resolution = 2.9 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= 0.009 sd= 0.199 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: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1665 5.49 5 Mg 1 5.21 5 S 181 5.16 5 C 40495 2.51 5 N 13743 2.21 5 O 18452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 36": "OE1" <-> "OE2" Residue "R GLU 87": "OE1" <-> "OE2" Residue "R GLU 94": "OE1" <-> "OE2" Residue "R GLU 97": "OE1" <-> "OE2" Residue "D ASP 14": "OD1" <-> "OD2" Residue "D ASP 162": "OD1" <-> "OD2" Residue "F GLU 106": "OE1" <-> "OE2" Residue "F GLU 197": "OE1" <-> "OE2" Residue "K GLU 60": "OE1" <-> "OE2" Residue "K PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 58": "OE1" <-> "OE2" Residue "P PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 52": "OE1" <-> "OE2" Residue "c GLU 64": "OE1" <-> "OE2" Residue "g ASP 260": "OD1" <-> "OD2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A ASP 158": "OD1" <-> "OD2" Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 32": "OD1" <-> "OD2" Residue "B ASP 108": "OD1" <-> "OD2" Residue "B ASP 196": "OD1" <-> "OD2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C ASP 220": "OD1" <-> "OD2" Residue "C ASP 221": "OD1" <-> "OD2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 151": "OD1" <-> "OD2" Residue "E PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 204": "OE1" <-> "OE2" Residue "H PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 127": "OD1" <-> "OD2" Residue "I ASP 80": "OD1" <-> "OD2" Residue "I TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 134": "OE1" <-> "OE2" Residue "J GLU 59": "OE1" <-> "OE2" Residue "J TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "J PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 158": "OD1" <-> "OD2" Residue "L TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 83": "OD1" <-> "OD2" Residue "O ASP 67": "OD1" <-> "OD2" Residue "O GLU 68": "OE1" <-> "OE2" Residue "O GLU 130": "OE1" <-> "OE2" Residue "W PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 112": "OD1" <-> "OD2" Residue "W GLU 115": "OE1" <-> "OE2" Residue "X TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Y ASP 77": "OD1" <-> "OD2" Residue "a ASP 52": "OD1" <-> "OD2" Residue "a GLU 90": "OE1" <-> "OE2" Residue "1 GLU 155": "OE1" <-> "OE2" Residue "1 PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 74540 Number of models: 1 Model: "" Number of chains: 40 Chain: "R" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 125} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "2" Number of atoms: 35552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1665, 35552 Classifications: {'RNA': 1665} Modifications used: {'rna2p_pur': 130, 'rna2p_pyr': 116, 'rna3p_pur': 754, 'rna3p_pyr': 665} Link IDs: {'rna2p': 246, 'rna3p': 1418} Chain breaks: 10 Chain: "d" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "D" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 213} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1495 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain: "K" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 800 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 7, 'TRANS': 87} Chain: "M" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "P" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 984 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "Q" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1109 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "S" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1184 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain: "T" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1122 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "U" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 795 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "Z" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "c" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 479 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "f" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 585 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "g" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2440 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 10, 'TRANS': 303} Chain: "A" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 12, 'TRANS': 193} Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "C" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1682 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 205} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "G" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1862 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain: "H" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1501 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 176} Chain: "I" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1682 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "J" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1499 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "L" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1229 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "N" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "O" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1006 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "W" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "X" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 135} Chain: "Y" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1014 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "a" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "b" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 640 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "e" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 397 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain breaks: 1 Chain: "h" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 231 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "1" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 250 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 36780 SG CYS d 21 156.729 161.688 70.501 1.00 7.48 S ATOM 36804 SG CYS d 24 154.114 159.191 69.450 1.00 7.48 S ATOM 36925 SG CYS d 39 153.047 162.255 71.573 1.00 16.59 S ATOM 36951 SG CYS d 42 154.823 159.555 73.156 1.00 7.48 S ATOM 48689 SG CYS f 121 181.580 153.417 26.012 1.00 27.28 S ATOM 48725 SG CYS f 126 181.007 152.109 29.524 1.00 32.32 S ATOM 48843 SG CYS f 141 178.076 153.064 27.044 1.00 23.42 S ATOM 48862 SG CYS f 144 179.975 155.599 28.964 1.00 23.63 S ATOM 72382 SG CYS a 23 86.706 166.586 109.736 1.00 7.48 S ATOM 72403 SG CYS a 26 87.072 165.932 105.851 1.00 9.58 S ATOM 72786 SG CYS a 74 88.677 163.550 108.492 1.00 7.48 S ATOM 72805 SG CYS a 77 89.787 166.976 107.325 1.00 8.38 S Time building chain proxies: 29.81, per 1000 atoms: 0.40 Number of scatterers: 74540 At special positions: 0 Unit cell: (216, 252.72, 208.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 181 16.00 P 1665 15.00 Mg 1 11.99 O 18452 8.00 N 13743 7.00 C 40495 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS b 40 " - pdb=" SG CYS b 59 " distance=2.03 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: 26.96 Conformation dependent library (CDL) restraints added in 4.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 201 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 77 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 26 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 74 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 23 " pdb=" ZN d 201 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 42 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 24 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 39 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 21 " pdb=" ZN f 500 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 141 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 144 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 126 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 121 " Number of angles added : 18 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9050 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 55 sheets defined 35.0% alpha, 19.1% beta 509 base pairs and 886 stacking pairs defined. Time for finding SS restraints: 21.16 Creating SS restraints... Processing helix chain 'R' and resid 6 through 20 Processing helix chain 'R' and resid 27 through 39 removed outlier: 3.775A pdb=" N ARG R 33 " --> pdb=" O HIS R 29 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU R 36 " --> pdb=" O LYS R 32 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU R 37 " --> pdb=" O ARG R 33 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 64 removed outlier: 3.592A pdb=" N THR R 55 " --> pdb=" O ALA R 51 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS R 59 " --> pdb=" O THR R 55 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG R 60 " --> pdb=" O HIS R 56 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN R 62 " --> pdb=" O MET R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 83 Processing helix chain 'R' and resid 99 through 109 removed outlier: 3.533A pdb=" N GLU R 104 " --> pdb=" O PRO R 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 15 through 19 Processing helix chain 'd' and resid 32 through 36 Processing helix chain 'd' and resid 40 through 51 removed outlier: 4.077A pdb=" N ARG d 44 " --> pdb=" O ARG d 40 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN d 45 " --> pdb=" O GLN d 41 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LYS d 48 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ASP d 49 " --> pdb=" O GLN d 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 30 removed outlier: 3.940A pdb=" N GLY D 15 " --> pdb=" O PHE D 11 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS D 18 " --> pdb=" O ASP D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.583A pdb=" N LEU D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 65 through 78 removed outlier: 3.815A pdb=" N ALA D 71 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN D 74 " --> pdb=" O THR D 70 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 105 through 110 Processing helix chain 'D' and resid 114 through 129 removed outlier: 3.539A pdb=" N PHE D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'F' and resid 18 through 22 Processing helix chain 'F' and resid 62 through 66 Processing helix chain 'F' and resid 67 through 76 removed outlier: 3.658A pdb=" N SER F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET F 76 " --> pdb=" O LEU F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.041A pdb=" N ASN F 83 " --> pdb=" O GLY F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 104 removed outlier: 3.634A pdb=" N THR F 89 " --> pdb=" O LYS F 85 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS F 101 " --> pdb=" O PHE F 97 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU F 102 " --> pdb=" O GLU F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 119 Processing helix chain 'F' and resid 142 through 161 Processing helix chain 'F' and resid 171 through 182 Processing helix chain 'F' and resid 187 through 203 removed outlier: 3.639A pdb=" N VAL F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 18 removed outlier: 3.977A pdb=" N LYS K 17 " --> pdb=" O GLU K 13 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU K 18 " --> pdb=" O LEU K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 36 removed outlier: 3.789A pdb=" N ALA K 36 " --> pdb=" O PRO K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 55 removed outlier: 3.776A pdb=" N VAL K 45 " --> pdb=" O PRO K 41 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER K 51 " --> pdb=" O LYS K 47 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG K 55 " --> pdb=" O SER K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 83 removed outlier: 3.639A pdb=" N GLN K 77 " --> pdb=" O ASN K 73 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR K 78 " --> pdb=" O GLU K 74 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP K 81 " --> pdb=" O GLN K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 95 removed outlier: 3.653A pdb=" N ARG K 95 " --> pdb=" O ALA K 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 22 removed outlier: 3.541A pdb=" N ALA M 17 " --> pdb=" O ASP M 13 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU M 18 " --> pdb=" O VAL M 14 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLN M 19 " --> pdb=" O ASN M 15 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU M 20 " --> pdb=" O THR M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 44 Processing helix chain 'M' and resid 58 through 72 removed outlier: 4.130A pdb=" N VAL M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS M 63 " --> pdb=" O PRO M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 90 removed outlier: 3.523A pdb=" N TRP M 88 " --> pdb=" O LYS M 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 132 Processing helix chain 'P' and resid 21 through 26 Processing helix chain 'P' and resid 29 through 36 removed outlier: 4.530A pdb=" N MET P 34 " --> pdb=" O GLU P 31 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN P 35 " --> pdb=" O GLN P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 48 Processing helix chain 'P' and resid 50 through 66 Processing helix chain 'P' and resid 86 through 90 Processing helix chain 'P' and resid 108 through 112 Processing helix chain 'P' and resid 116 through 120 removed outlier: 3.582A pdb=" N SER P 120 " --> pdb=" O GLY P 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 42 No H-bonds generated for 'chain 'Q' and resid 40 through 42' Processing helix chain 'Q' and resid 47 through 59 removed outlier: 3.899A pdb=" N LEU Q 51 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Proline residue: Q 54 - end of helix Processing helix chain 'Q' and resid 76 through 96 removed outlier: 3.537A pdb=" N GLN Q 86 " --> pdb=" O TYR Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 116 removed outlier: 3.588A pdb=" N GLU Q 107 " --> pdb=" O ALA Q 103 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR Q 115 " --> pdb=" O ILE Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 120 Processing helix chain 'S' and resid 25 through 30 removed outlier: 3.868A pdb=" N ILE S 30 " --> pdb=" O ILE S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 31 through 33 No H-bonds generated for 'chain 'S' and resid 31 through 33' Processing helix chain 'S' and resid 39 through 48 removed outlier: 3.539A pdb=" N VAL S 43 " --> pdb=" O ARG S 39 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU S 45 " --> pdb=" O ALA S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 73 Processing helix chain 'S' and resid 74 through 78 Processing helix chain 'S' and resid 80 through 84 removed outlier: 3.800A pdb=" N LEU S 84 " --> pdb=" O ASP S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 104 removed outlier: 4.177A pdb=" N ASP S 104 " --> pdb=" O ALA S 100 " (cutoff:3.500A) Processing helix chain 'S' and resid 107 through 117 removed outlier: 3.621A pdb=" N LEU S 114 " --> pdb=" O ASP S 110 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 128 Processing helix chain 'T' and resid 11 through 24 removed outlier: 3.784A pdb=" N ARG T 16 " --> pdb=" O GLN T 12 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA T 20 " --> pdb=" O ARG T 16 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS T 23 " --> pdb=" O ALA T 19 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS T 24 " --> pdb=" O ALA T 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 67 Processing helix chain 'T' and resid 73 through 79 removed outlier: 3.638A pdb=" N ILE T 78 " --> pdb=" O SER T 74 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR T 79 " --> pdb=" O MET T 75 " (cutoff:3.500A) Processing helix chain 'T' and resid 96 through 103 Processing helix chain 'T' and resid 124 through 145 removed outlier: 3.682A pdb=" N GLN T 137 " --> pdb=" O ARG T 133 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 46 Processing helix chain 'U' and resid 94 through 99 Processing helix chain 'U' and resid 100 through 105 Processing helix chain 'Z' and resid 51 through 61 Processing helix chain 'Z' and resid 62 through 65 Processing helix chain 'Z' and resid 69 through 78 removed outlier: 3.963A pdb=" N GLU Z 75 " --> pdb=" O ALA Z 71 " (cutoff:3.500A) Processing helix chain 'Z' and resid 80 through 94 removed outlier: 3.984A pdb=" N GLN Z 89 " --> pdb=" O ARG Z 85 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU Z 90 " --> pdb=" O ALA Z 86 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU Z 91 " --> pdb=" O ALA Z 87 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU Z 92 " --> pdb=" O LEU Z 88 " (cutoff:3.500A) Processing helix chain 'f' and resid 102 through 104 No H-bonds generated for 'chain 'f' and resid 102 through 104' Processing helix chain 'A' and resid 11 through 21 removed outlier: 3.515A pdb=" N LYS A 17 " --> pdb=" O GLU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 50 through 67 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 83 through 95 removed outlier: 3.635A pdb=" N LEU A 88 " --> pdb=" O GLN A 84 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 93 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 136 removed outlier: 3.605A pdb=" N LEU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 167 through 187 Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'B' and resid 23 through 26 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 106 through 114 Processing helix chain 'B' and resid 157 through 178 removed outlier: 3.572A pdb=" N THR B 173 " --> pdb=" O MET B 169 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 176 " --> pdb=" O MET B 172 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 189 removed outlier: 3.570A pdb=" N ASN B 186 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 200 removed outlier: 3.716A pdb=" N LYS B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 231 removed outlier: 3.629A pdb=" N MET B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU B 230 " --> pdb=" O GLY B 226 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B 231 " --> pdb=" O LYS B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 225 through 231' Processing helix chain 'C' and resid 66 through 71 Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'C' and resid 90 through 98 removed outlier: 4.218A pdb=" N ILE C 94 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 102 Processing helix chain 'C' and resid 146 through 161 removed outlier: 3.738A pdb=" N ILE C 156 " --> pdb=" O ARG C 152 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 217 removed outlier: 3.721A pdb=" N LYS C 212 " --> pdb=" O PRO C 208 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU C 213 " --> pdb=" O VAL C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 246 removed outlier: 3.508A pdb=" N THR C 240 " --> pdb=" O PHE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.674A pdb=" N TRP C 256 " --> pdb=" O PRO C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'C' and resid 269 through 276 Processing helix chain 'E' and resid 10 through 14 Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 37 through 41 removed outlier: 4.219A pdb=" N CYS E 41 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 49 Processing helix chain 'E' and resid 57 through 66 removed outlier: 3.519A pdb=" N VAL E 61 " --> pdb=" O THR E 57 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS E 62 " --> pdb=" O GLY E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 247 through 262 removed outlier: 3.655A pdb=" N ALA E 258 " --> pdb=" O LYS E 254 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS E 259 " --> pdb=" O ARG E 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 28 removed outlier: 4.416A pdb=" N THR G 26 " --> pdb=" O ARG G 22 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE G 27 " --> pdb=" O LYS G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 181 through 230 removed outlier: 3.682A pdb=" N ASN G 202 " --> pdb=" O ARG G 198 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA G 207 " --> pdb=" O LYS G 203 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA G 210 " --> pdb=" O ALA G 206 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS G 211 " --> pdb=" O ALA G 207 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU G 222 " --> pdb=" O LYS G 218 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS G 223 " --> pdb=" O GLU G 219 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG G 224 " --> pdb=" O ALA G 220 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN G 227 " --> pdb=" O LYS G 223 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA G 229 " --> pdb=" O GLN G 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 34 removed outlier: 3.750A pdb=" N ILE H 23 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER H 24 " --> pdb=" O GLU H 20 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU H 29 " --> pdb=" O GLN H 25 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU H 30 " --> pdb=" O ALA H 26 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N MET H 32 " --> pdb=" O LEU H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 74 Processing helix chain 'H' and resid 75 through 84 Processing helix chain 'H' and resid 117 through 120 Processing helix chain 'H' and resid 121 through 134 removed outlier: 3.918A pdb=" N GLU H 131 " --> pdb=" O ASP H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 167 Processing helix chain 'H' and resid 169 through 181 removed outlier: 3.560A pdb=" N GLY H 175 " --> pdb=" O GLU H 171 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS H 179 " --> pdb=" O GLY H 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 106 through 117 Processing helix chain 'I' and resid 130 through 138 Processing helix chain 'I' and resid 142 through 151 Processing helix chain 'I' and resid 152 through 156 removed outlier: 3.591A pdb=" N ASN I 155 " --> pdb=" O ARG I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 166 removed outlier: 3.639A pdb=" N GLN I 165 " --> pdb=" O LEU I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 183 Processing helix chain 'I' and resid 191 through 204 removed outlier: 3.501A pdb=" N LYS I 201 " --> pdb=" O PHE I 197 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS I 203 " --> pdb=" O LEU I 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 36 Processing helix chain 'J' and resid 40 through 61 removed outlier: 4.084A pdb=" N VAL J 46 " --> pdb=" O GLU J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 84 removed outlier: 3.783A pdb=" N ASN J 75 " --> pdb=" O LEU J 71 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE J 84 " --> pdb=" O ARG J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 92 removed outlier: 4.169A pdb=" N MET J 92 " --> pdb=" O GLU J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 107 removed outlier: 3.684A pdb=" N PHE J 105 " --> pdb=" O LYS J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 117 removed outlier: 3.550A pdb=" N PHE J 115 " --> pdb=" O GLN J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 132 removed outlier: 3.711A pdb=" N ARG J 127 " --> pdb=" O ILE J 123 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL J 128 " --> pdb=" O HIS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 155 removed outlier: 5.934A pdb=" N LYS J 155 " --> pdb=" O ASP J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 179 Processing helix chain 'L' and resid 23 through 30 removed outlier: 3.665A pdb=" N LYS L 30 " --> pdb=" O GLY L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 52 removed outlier: 3.773A pdb=" N ILE L 51 " --> pdb=" O PRO L 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 42 Processing helix chain 'N' and resid 46 through 59 removed outlier: 3.859A pdb=" N GLY N 59 " --> pdb=" O ARG N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 67 Processing helix chain 'N' and resid 70 through 79 Processing helix chain 'N' and resid 85 through 102 Processing helix chain 'N' and resid 108 through 132 removed outlier: 3.723A pdb=" N LYS N 112 " --> pdb=" O ASP N 108 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE N 113 " --> pdb=" O LYS N 109 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE N 116 " --> pdb=" O LYS N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 150 removed outlier: 3.884A pdb=" N LEU N 149 " --> pdb=" O THR N 145 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 68 Processing helix chain 'O' and resid 72 through 86 removed outlier: 3.638A pdb=" N ARG O 84 " --> pdb=" O ASP O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 122 removed outlier: 4.569A pdb=" N SER O 114 " --> pdb=" O PRO O 110 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU O 116 " --> pdb=" O ALA O 112 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG O 117 " --> pdb=" O GLN O 113 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU O 119 " --> pdb=" O ALA O 115 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA O 120 " --> pdb=" O LEU O 116 " (cutoff:3.500A) Processing helix chain 'V' and resid 56 through 62 Processing helix chain 'V' and resid 64 through 76 Processing helix chain 'W' and resid 5 through 20 removed outlier: 3.595A pdb=" N ASP W 9 " --> pdb=" O ASN W 5 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG W 20 " --> pdb=" O ASN W 16 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 44 removed outlier: 3.792A pdb=" N HIS W 44 " --> pdb=" O VAL W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 94 removed outlier: 3.591A pdb=" N TRP W 89 " --> pdb=" O ASP W 85 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 120 Processing helix chain 'X' and resid 9 through 22 removed outlier: 4.024A pdb=" N TRP X 22 " --> pdb=" O ARG X 18 " (cutoff:3.500A) Processing helix chain 'X' and resid 24 through 33 removed outlier: 4.508A pdb=" N GLY X 33 " --> pdb=" O LYS X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 33 through 38 Processing helix chain 'X' and resid 89 through 94 Processing helix chain 'X' and resid 130 through 135 Processing helix chain 'Y' and resid 36 through 49 removed outlier: 3.574A pdb=" N LYS Y 43 " --> pdb=" O GLU Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 53 No H-bonds generated for 'chain 'Y' and resid 51 through 53' Processing helix chain 'Y' and resid 78 through 86 Processing helix chain 'Y' and resid 87 through 93 removed outlier: 3.629A pdb=" N ALA Y 92 " --> pdb=" O LYS Y 88 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG Y 93 " --> pdb=" O HIS Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 103 through 115 removed outlier: 3.687A pdb=" N LYS Y 115 " --> pdb=" O LYS Y 111 " (cutoff:3.500A) Processing helix chain 'Y' and resid 119 through 123 Processing helix chain 'a' and resid 49 through 55 removed outlier: 3.918A pdb=" N GLU a 55 " --> pdb=" O ARG a 51 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 81 removed outlier: 3.579A pdb=" N ILE a 79 " --> pdb=" O VAL a 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 94 Processing helix chain 'b' and resid 11 through 18 removed outlier: 3.695A pdb=" N ARG b 17 " --> pdb=" O GLU b 13 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS b 18 " --> pdb=" O GLU b 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 10 through 16 Processing helix chain 'e' and resid 32 through 42 Processing helix chain 'h' and resid 3 through 21 removed outlier: 3.750A pdb=" N LYS h 19 " --> pdb=" O ARG h 15 " (cutoff:3.500A) Processing helix chain '1' and resid 152 through 160 Processing helix chain '1' and resid 165 through 178 Processing sheet with id=AA1, first strand: chain 'R' and resid 96 through 98 Processing sheet with id=AA2, first strand: chain 'd' and resid 30 through 31 removed outlier: 3.748A pdb=" N MET d 38 " --> pdb=" O ILE d 31 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'U' and resid 50 through 55 removed outlier: 3.527A pdb=" N ASP U 90 " --> pdb=" O LYS U 51 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU U 88 " --> pdb=" O PRO U 53 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ARG U 55 " --> pdb=" O LYS U 86 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LYS U 86 " --> pdb=" O ARG U 55 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 34 through 41 removed outlier: 3.678A pdb=" N GLY D 36 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR D 46 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N TYR D 87 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE D 48 " --> pdb=" O TYR D 87 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N GLU D 89 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE D 50 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 146 through 155 removed outlier: 8.221A pdb=" N ARG D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU D 142 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LYS D 141 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL D 181 " --> pdb=" O LYS D 141 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 223 through 225 removed outlier: 4.675A pdb=" N LEU g 173 " --> pdb=" O GLY g 169 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY g 169 " --> pdb=" O LEU g 173 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS g 175 " --> pdb=" O SER g 167 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS g 153 " --> pdb=" O CYS g 168 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 123 through 127 Processing sheet with id=AA9, first strand: chain 'K' and resid 20 through 24 Processing sheet with id=AB1, first strand: chain 'M' and resid 75 through 78 removed outlier: 6.591A pdb=" N CYS M 50 " --> pdb=" O ILE M 77 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU M 49 " --> pdb=" O VAL M 111 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 76 through 78 removed outlier: 3.715A pdb=" N GLY P 95 " --> pdb=" O VAL P 76 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 10 through 15 removed outlier: 6.821A pdb=" N LYS Q 33 " --> pdb=" O VAL Q 70 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL Q 72 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 12 through 14 Processing sheet with id=AB5, first strand: chain 'T' and resid 81 through 83 Processing sheet with id=AB6, first strand: chain 'T' and resid 113 through 115 Processing sheet with id=AB7, first strand: chain 'Z' and resid 98 through 101 removed outlier: 5.764A pdb=" N LEU Z 99 " --> pdb=" O THR Z 110 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR Z 110 " --> pdb=" O LEU Z 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'c' and resid 41 through 47 removed outlier: 7.080A pdb=" N CYS c 27 " --> pdb=" O GLY c 19 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLY c 19 " --> pdb=" O CYS c 27 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N GLN c 29 " --> pdb=" O VAL c 17 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N VAL c 17 " --> pdb=" O GLN c 29 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ARG c 31 " --> pdb=" O THR c 15 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'f' and resid 106 through 108 Processing sheet with id=AC1, first strand: chain 'f' and resid 133 through 134 Processing sheet with id=AC2, first strand: chain 'g' and resid 5 through 11 removed outlier: 6.302A pdb=" N LEU g 7 " --> pdb=" O GLN g 311 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLN g 311 " --> pdb=" O LEU g 7 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY g 9 " --> pdb=" O VAL g 309 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER g 288 " --> pdb=" O GLY g 301 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'g' and resid 18 through 23 removed outlier: 3.588A pdb=" N ILE g 31 " --> pdb=" O TRP g 43 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG g 57 " --> pdb=" O MET g 42 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LYS g 44 " --> pdb=" O PRO g 55 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'g' and resid 66 through 71 removed outlier: 3.857A pdb=" N ARG g 99 " --> pdb=" O LEU g 89 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'g' and resid 108 through 113 removed outlier: 3.549A pdb=" N GLY g 123 " --> pdb=" O SER g 110 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU g 131 " --> pdb=" O LYS g 139 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'g' and resid 195 through 200 removed outlier: 3.550A pdb=" N THR g 197 " --> pdb=" O GLY g 210 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET g 217 " --> pdb=" O SER g 209 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY g 211 " --> pdb=" O GLN g 215 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLN g 215 " --> pdb=" O GLY g 211 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ASP g 220 " --> pdb=" O HIS g 226 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N HIS g 226 " --> pdb=" O ASP g 220 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'g' and resid 240 through 241 removed outlier: 6.344A pdb=" N ILE g 256 " --> pdb=" O GLU g 269 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU g 269 " --> pdb=" O ILE g 256 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE g 258 " --> pdb=" O VAL g 267 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 38 through 42 removed outlier: 6.872A pdb=" N ILE A 48 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ARG A 41 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE A 46 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.820A pdb=" N VAL A 74 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ILE A 99 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A 76 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU A 122 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N LEU A 147 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL A 124 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR A 144 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ILE A 161 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ALA A 146 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 43 through 50 removed outlier: 4.078A pdb=" N GLY B 45 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N CYS B 96 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP B 32 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N THR B 98 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LYS B 34 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N PHE B 100 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASN B 95 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL B 91 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU B 97 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LYS B 85 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N MET B 103 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS B 83 " --> pdb=" O MET B 103 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 43 through 50 removed outlier: 4.078A pdb=" N GLY B 45 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N CYS B 96 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP B 32 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N THR B 98 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LYS B 34 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N PHE B 100 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 12.757A pdb=" N ASN B 99 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 12.728A pdb=" N LYS B 219 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N HIS B 101 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET B 217 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ARG B 213 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N VAL B 212 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL B 140 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS B 214 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 103 through 116 removed outlier: 5.282A pdb=" N ASP C 104 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLY C 131 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL C 106 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS C 108 " --> pdb=" O PHE C 127 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY C 119 " --> pdb=" O THR C 116 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 184 through 188 Processing sheet with id=AD5, first strand: chain 'E' and resid 42 through 43 removed outlier: 3.534A pdb=" N ALA E 84 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.504A pdb=" N LYS E 75 " --> pdb=" O ILE E 72 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N HIS E 112 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE E 102 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.077A pdb=" N ASP E 171 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE E 169 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 217 through 221 removed outlier: 6.376A pdb=" N VAL E 207 " --> pdb=" O ARG E 198 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ARG E 198 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N HIS E 209 " --> pdb=" O THR E 196 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 13 through 17 removed outlier: 6.936A pdb=" N LYS G 2 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N LEU G 111 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASN G 4 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE G 113 " --> pdb=" O ASN G 4 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N SER G 6 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N LYS G 115 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN G 56 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LEU G 109 " --> pdb=" O GLY G 54 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLY G 54 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU G 111 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ILE G 52 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE G 113 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL G 50 " --> pdb=" O ILE G 113 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 72 through 77 Processing sheet with id=AE2, first strand: chain 'G' and resid 160 through 162 removed outlier: 3.994A pdb=" N ARG G 170 " --> pdb=" O LEU G 162 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 47 through 53 removed outlier: 3.572A pdb=" N HIS H 91 " --> pdb=" O LYS H 58 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 184 through 188 removed outlier: 4.660A pdb=" N ASP H 184 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY H 141 " --> pdb=" O HIS H 157 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 37 through 38 removed outlier: 6.405A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 62 through 67 removed outlier: 5.895A pdb=" N ARG I 77 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU I 103 " --> pdb=" O ILE I 79 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N VAL I 81 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ILE I 101 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N CYS I 100 " --> pdb=" O ILE I 175 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N GLY I 187 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN I 64 " --> pdb=" O GLY I 187 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL I 189 " --> pdb=" O ASN I 64 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N SER I 66 " --> pdb=" O VAL I 189 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 140 through 141 Processing sheet with id=AE8, first strand: chain 'L' and resid 72 through 79 removed outlier: 16.743A pdb=" N LEU L 73 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 15.725A pdb=" N LEU L 93 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N GLY L 75 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N ASP L 91 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL L 77 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ARG L 89 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 16.107A pdb=" N VAL L 138 " --> pdb=" O HIS L 106 " (cutoff:3.500A) removed outlier: 14.018A pdb=" N ASN L 108 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 10.436A pdb=" N PHE L 140 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N SER L 110 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL L 142 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N HIS L 112 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N LYS L 144 " --> pdb=" O HIS L 112 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR L 127 " --> pdb=" O LEU L 143 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL L 145 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE L 125 " --> pdb=" O VAL L 145 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 52 through 57 removed outlier: 6.720A pdb=" N VAL O 44 " --> pdb=" O ILE O 53 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG O 55 " --> pdb=" O VAL O 42 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL O 42 " --> pdb=" O ARG O 55 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR O 57 " --> pdb=" O THR O 40 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR O 40 " --> pdb=" O THR O 57 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU O 93 " --> pdb=" O GLY O 127 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE O 129 " --> pdb=" O LEU O 93 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE O 95 " --> pdb=" O ILE O 129 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ASP O 131 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU O 97 " --> pdb=" O ASP O 131 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'V' and resid 15 through 16 removed outlier: 4.323A pdb=" N ARG V 15 " --> pdb=" O ILE V 24 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'V' and resid 32 through 39 removed outlier: 6.541A pdb=" N ILE V 32 " --> pdb=" O TYR V 53 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TYR V 53 " --> pdb=" O ILE V 32 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N MET V 34 " --> pdb=" O LYS V 51 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LYS V 51 " --> pdb=" O MET V 34 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL V 36 " --> pdb=" O GLN V 49 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN V 49 " --> pdb=" O VAL V 36 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N GLU V 38 " --> pdb=" O ASN V 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'W' and resid 71 through 74 Processing sheet with id=AF4, first strand: chain 'W' and resid 71 through 74 removed outlier: 6.730A pdb=" N VAL W 103 " --> pdb=" O LEU W 126 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N PHE W 128 " --> pdb=" O PHE W 101 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE W 101 " --> pdb=" O PHE W 128 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'X' and resid 128 through 129 removed outlier: 6.574A pdb=" N LEU X 101 " --> pdb=" O VAL X 123 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N VAL X 125 " --> pdb=" O GLU X 99 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLU X 99 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL X 51 " --> pdb=" O GLN X 73 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLN X 73 " --> pdb=" O VAL X 51 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU X 53 " --> pdb=" O ARG X 71 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE X 120 " --> pdb=" O THR X 82 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Y' and resid 6 through 15 removed outlier: 5.775A pdb=" N ILE Y 7 " --> pdb=" O LEU Y 28 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU Y 28 " --> pdb=" O ILE Y 7 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N THR Y 9 " --> pdb=" O ASP Y 26 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASP Y 26 " --> pdb=" O THR Y 9 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LYS Y 11 " --> pdb=" O VAL Y 24 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL Y 24 " --> pdb=" O LYS Y 11 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE Y 72 " --> pdb=" O GLY Y 59 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLY Y 59 " --> pdb=" O PHE Y 72 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N MET Y 74 " --> pdb=" O VAL Y 57 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N VAL Y 57 " --> pdb=" O MET Y 74 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N TYR Y 76 " --> pdb=" O ILE Y 55 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE Y 55 " --> pdb=" O TYR Y 76 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=AF8, first strand: chain 'a' and resid 36 through 43 Processing sheet with id=AF9, first strand: chain 'b' and resid 32 through 36 Processing sheet with id=AG1, first strand: chain 'b' and resid 64 through 65 1388 hydrogen bonds defined for protein. 3858 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1271 hydrogen bonds 2022 hydrogen bond angles 0 basepair planarities 509 basepair parallelities 886 stacking parallelities Total time for adding SS restraints: 57.94 Time building geometry restraints manager: 29.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 14414 1.33 - 1.45: 27196 1.45 - 1.58: 34194 1.58 - 1.70: 3320 1.70 - 1.82: 275 Bond restraints: 79399 Sorted by residual: bond pdb=" CA LEU d 6 " pdb=" CB LEU d 6 " ideal model delta sigma weight residual 1.539 1.608 -0.069 4.88e-02 4.20e+02 1.99e+00 bond pdb=" CB PRO f 88 " pdb=" CG PRO f 88 " ideal model delta sigma weight residual 1.492 1.560 -0.068 5.00e-02 4.00e+02 1.87e+00 bond pdb=" C ARG D 64 " pdb=" N ARG D 65 " ideal model delta sigma weight residual 1.331 1.312 0.018 1.38e-02 5.25e+03 1.73e+00 bond pdb=" CB VAL c 55 " pdb=" CG1 VAL c 55 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.67e+00 bond pdb=" C3' C 21403 " pdb=" O3' C 21403 " ideal model delta sigma weight residual 1.427 1.446 -0.019 1.50e-02 4.44e+03 1.61e+00 ... (remaining 79394 not shown) Histogram of bond angle deviations from ideal: 99.25 - 106.45: 10493 106.45 - 113.64: 46810 113.64 - 120.84: 33256 120.84 - 128.04: 21780 128.04 - 135.24: 2795 Bond angle restraints: 115134 Sorted by residual: angle pdb=" N GLU F 171 " pdb=" CA GLU F 171 " pdb=" C GLU F 171 " ideal model delta sigma weight residual 114.04 107.80 6.24 1.24e+00 6.50e-01 2.53e+01 angle pdb=" C ASP g 304 " pdb=" N ASN g 305 " pdb=" CA ASN g 305 " ideal model delta sigma weight residual 123.93 130.35 -6.42 1.54e+00 4.22e-01 1.74e+01 angle pdb=" C3' C 21403 " pdb=" O3' C 21403 " pdb=" P U 21404 " ideal model delta sigma weight residual 120.20 126.11 -5.91 1.50e+00 4.44e-01 1.55e+01 angle pdb=" C3' G 2 114 " pdb=" O3' G 2 114 " pdb=" P U 2 115 " ideal model delta sigma weight residual 120.20 126.06 -5.86 1.50e+00 4.44e-01 1.52e+01 angle pdb=" C4' G 21648 " pdb=" C3' G 21648 " pdb=" O3' G 21648 " ideal model delta sigma weight residual 109.40 115.21 -5.81 1.50e+00 4.44e-01 1.50e+01 ... (remaining 115129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 42979 35.98 - 71.95: 1394 71.95 - 107.93: 93 107.93 - 143.90: 26 143.90 - 179.88: 29 Dihedral angle restraints: 44521 sinusoidal: 30492 harmonic: 14029 Sorted by residual: dihedral pdb=" O4' U 2 427 " pdb=" C1' U 2 427 " pdb=" N1 U 2 427 " pdb=" C2 U 2 427 " ideal model delta sinusoidal sigma weight residual -160.00 18.74 -178.74 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 2 853 " pdb=" C1' C 2 853 " pdb=" N1 C 2 853 " pdb=" C2 C 2 853 " ideal model delta sinusoidal sigma weight residual -160.00 18.30 -178.30 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 21139 " pdb=" C1' C 21139 " pdb=" N1 C 21139 " pdb=" C2 C 21139 " ideal model delta sinusoidal sigma weight residual 200.00 26.52 173.48 1 1.50e+01 4.44e-03 8.51e+01 ... (remaining 44518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 12372 0.057 - 0.114: 1573 0.114 - 0.171: 217 0.171 - 0.228: 39 0.228 - 0.285: 10 Chirality restraints: 14211 Sorted by residual: chirality pdb=" C3' G 2 114 " pdb=" C4' G 2 114 " pdb=" O3' G 2 114 " pdb=" C2' G 2 114 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C1' G 21632 " pdb=" O4' G 21632 " pdb=" C2' G 21632 " pdb=" N9 G 21632 " both_signs ideal model delta sigma weight residual False 2.46 2.20 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C1' A 2 25 " pdb=" O4' A 2 25 " pdb=" C2' A 2 25 " pdb=" N9 A 2 25 " both_signs ideal model delta sigma weight residual False 2.46 2.21 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 14208 not shown) Planarity restraints: 8425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 205 " 0.025 2.00e-02 2.50e+03 2.56e-02 1.31e+01 pdb=" CG TYR B 205 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR B 205 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 205 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 205 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B 205 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR B 205 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 205 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR f 87 " 0.059 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO f 88 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO f 88 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO f 88 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 33 " 0.283 9.50e-02 1.11e+02 1.27e-01 9.95e+00 pdb=" NE ARG M 33 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG M 33 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG M 33 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG M 33 " 0.012 2.00e-02 2.50e+03 ... (remaining 8422 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 1097 2.61 - 3.18: 56233 3.18 - 3.75: 128483 3.75 - 4.33: 188830 4.33 - 4.90: 268458 Nonbonded interactions: 643101 Sorted by model distance: nonbonded pdb=" OG SER g 114 " pdb=" OD1 ASP g 116 " model vdw 2.031 2.440 nonbonded pdb=" OP2 A 2 103 " pdb=" N4 C 2 356 " model vdw 2.096 2.520 nonbonded pdb=" OE1 GLN c 29 " pdb=" ND2 ASN c 45 " model vdw 2.096 2.520 nonbonded pdb=" O2' C 21374 " pdb=" O2 C 21464 " model vdw 2.106 2.440 nonbonded pdb=" O2' A 21569 " pdb=" O2' C 21626 " model vdw 2.112 2.440 ... (remaining 643096 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 14.330 Check model and map are aligned: 0.850 Set scattering table: 0.520 Process input model: 203.250 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.220 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: 0.020 Load rotamer database and sin/cos tables:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 236.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 : 0.004 0.069 79399 Z= 0.221 Angle : 0.626 10.894 115134 Z= 0.333 Chirality : 0.040 0.285 14211 Planarity : 0.005 0.127 8425 Dihedral : 15.786 179.878 35468 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.68 % Favored : 96.30 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.11), residues: 4809 helix: -1.25 (0.13), residues: 1467 sheet: 0.09 (0.17), residues: 869 loop : -0.80 (0.12), residues: 2473 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 711 time to evaluate : 4.685 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 711 average time/residue: 1.8316 time to fit residues: 1664.0890 Evaluate side-chains 582 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 582 time to evaluate : 4.536 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 542 optimal weight: 0.8980 chunk 486 optimal weight: 2.9990 chunk 270 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 328 optimal weight: 4.9990 chunk 259 optimal weight: 20.0000 chunk 503 optimal weight: 8.9990 chunk 194 optimal weight: 4.9990 chunk 305 optimal weight: 4.9990 chunk 374 optimal weight: 5.9990 chunk 583 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 83 ASN F 186 ASN K 73 ASN P 103 ASN Q 48 GLN ** T 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 28 ASN c 29 GLN g 191 HIS H 165 ASN J 154 GLN L 112 HIS N 62 GLN O 103 ASN e 44 ASN 1 160 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.0717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 79399 Z= 0.335 Angle : 0.701 12.036 115134 Z= 0.362 Chirality : 0.045 0.313 14211 Planarity : 0.006 0.092 8425 Dihedral : 15.441 179.045 25375 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.20 % Favored : 95.78 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.11), residues: 4809 helix: -0.76 (0.13), residues: 1487 sheet: 0.01 (0.17), residues: 898 loop : -0.86 (0.12), residues: 2424 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 603 time to evaluate : 4.570 Fit side-chains revert: symmetry clash outliers start: 95 outliers final: 48 residues processed: 645 average time/residue: 1.7909 time to fit residues: 1486.6497 Evaluate side-chains 630 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 582 time to evaluate : 4.511 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 26 residues processed: 22 average time/residue: 0.9100 time to fit residues: 36.5170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 324 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 485 optimal weight: 7.9990 chunk 396 optimal weight: 0.7980 chunk 160 optimal weight: 6.9990 chunk 584 optimal weight: 1.9990 chunk 630 optimal weight: 7.9990 chunk 520 optimal weight: 3.9990 chunk 579 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 chunk 468 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 73 ASN P 103 ASN T 11 GLN U 28 ASN Z 46 ASN ** g 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 9 GLN H 97 GLN H 165 ASN I 168 GLN J 154 GLN N 36 GLN O 103 ASN W 15 ASN 1 160 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.0753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 79399 Z= 0.156 Angle : 0.566 10.351 115134 Z= 0.296 Chirality : 0.038 0.273 14211 Planarity : 0.004 0.092 8425 Dihedral : 15.269 179.873 25375 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.31 % Favored : 96.67 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.12), residues: 4809 helix: -0.15 (0.13), residues: 1489 sheet: 0.20 (0.17), residues: 865 loop : -0.79 (0.12), residues: 2455 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 621 time to evaluate : 4.605 Fit side-chains revert: symmetry clash outliers start: 88 outliers final: 46 residues processed: 666 average time/residue: 1.8368 time to fit residues: 1580.1982 Evaluate side-chains 644 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 598 time to evaluate : 4.603 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 29 residues processed: 18 average time/residue: 1.0486 time to fit residues: 33.9210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 577 optimal weight: 3.9990 chunk 439 optimal weight: 0.7980 chunk 303 optimal weight: 0.0970 chunk 64 optimal weight: 7.9990 chunk 278 optimal weight: 8.9990 chunk 392 optimal weight: 5.9990 chunk 586 optimal weight: 0.9990 chunk 620 optimal weight: 1.9990 chunk 306 optimal weight: 10.0000 chunk 555 optimal weight: 0.0170 chunk 167 optimal weight: 10.0000 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 73 ASN P 103 ASN ** T 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 28 ASN Z 46 ASN c 29 GLN c 45 ASN ** g 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 9 GLN H 165 ASN I 111 GLN I 168 GLN J 154 GLN N 36 GLN O 103 ASN X 63 ASN 1 160 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.073 79399 Z= 0.133 Angle : 0.527 9.904 115134 Z= 0.274 Chirality : 0.036 0.253 14211 Planarity : 0.004 0.093 8425 Dihedral : 15.101 179.221 25375 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.26 % Favored : 96.71 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % 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: -0.34 (0.12), residues: 4809 helix: 0.27 (0.14), residues: 1490 sheet: 0.26 (0.17), residues: 888 loop : -0.66 (0.12), residues: 2431 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 630 time to evaluate : 5.577 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 51 residues processed: 687 average time/residue: 1.7722 time to fit residues: 1583.9112 Evaluate side-chains 643 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 592 time to evaluate : 4.635 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 38 residues processed: 14 average time/residue: 0.8508 time to fit residues: 25.1169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 516 optimal weight: 3.9990 chunk 352 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 462 optimal weight: 5.9990 chunk 256 optimal weight: 10.0000 chunk 529 optimal weight: 1.9990 chunk 428 optimal weight: 0.0970 chunk 0 optimal weight: 7.9990 chunk 316 optimal weight: 8.9990 chunk 557 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 73 ASN U 28 ASN ** g 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 133 ASN g 181 ASN H 97 GLN H 165 ASN H 168 HIS I 168 GLN J 154 GLN L 13 GLN N 36 GLN O 103 ASN V 49 GLN X 63 ASN h 22 GLN 1 160 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 79399 Z= 0.183 Angle : 0.560 11.386 115134 Z= 0.290 Chirality : 0.038 0.269 14211 Planarity : 0.004 0.094 8425 Dihedral : 15.083 179.862 25375 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.66 % Favored : 96.32 % Rotamer Outliers : 2.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % 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: -0.26 (0.12), residues: 4809 helix: 0.40 (0.14), residues: 1488 sheet: 0.32 (0.17), residues: 889 loop : -0.66 (0.12), residues: 2432 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 590 time to evaluate : 4.574 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 63 residues processed: 649 average time/residue: 1.7579 time to fit residues: 1485.9846 Evaluate side-chains 646 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 583 time to evaluate : 4.520 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 44 residues processed: 20 average time/residue: 0.9732 time to fit residues: 35.4417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 208 optimal weight: 10.0000 chunk 558 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 364 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 621 optimal weight: 5.9990 chunk 515 optimal weight: 0.7980 chunk 287 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 205 optimal weight: 0.0000 chunk 326 optimal weight: 6.9990 overall best weight: 3.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 73 ASN U 28 ASN ** g 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 GLN I 168 GLN J 154 GLN N 36 GLN O 83 GLN O 103 ASN V 49 GLN W 15 ASN X 63 ASN ** e 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 160 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.069 79399 Z= 0.383 Angle : 0.727 12.581 115134 Z= 0.371 Chirality : 0.047 0.325 14211 Planarity : 0.006 0.095 8425 Dihedral : 15.390 179.003 25375 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.16 % Favored : 95.82 % Rotamer Outliers : 3.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.60 (0.12), residues: 4809 helix: 0.04 (0.13), residues: 1484 sheet: 0.12 (0.17), residues: 901 loop : -0.81 (0.12), residues: 2424 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 607 time to evaluate : 4.772 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 153 outliers final: 82 residues processed: 698 average time/residue: 1.8260 time to fit residues: 1649.9793 Evaluate side-chains 677 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 595 time to evaluate : 4.537 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 60 residues processed: 23 average time/residue: 0.8934 time to fit residues: 37.7488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 598 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 353 optimal weight: 6.9990 chunk 453 optimal weight: 5.9990 chunk 351 optimal weight: 7.9990 chunk 522 optimal weight: 1.9990 chunk 346 optimal weight: 10.0000 chunk 618 optimal weight: 2.9990 chunk 387 optimal weight: 1.9990 chunk 377 optimal weight: 1.9990 chunk 285 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 73 ASN U 28 ASN ** g 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 181 ASN A 9 GLN H 97 GLN I 168 GLN J 154 GLN O 83 GLN O 103 ASN V 49 GLN ** e 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 160 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 79399 Z= 0.231 Angle : 0.619 10.709 115134 Z= 0.322 Chirality : 0.041 0.296 14211 Planarity : 0.005 0.095 8425 Dihedral : 15.308 179.240 25375 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.83 % Favored : 96.15 % Rotamer Outliers : 2.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.12), residues: 4809 helix: 0.20 (0.14), residues: 1489 sheet: 0.15 (0.17), residues: 892 loop : -0.78 (0.12), residues: 2428 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 605 time to evaluate : 4.694 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 85 residues processed: 681 average time/residue: 1.7757 time to fit residues: 1564.0645 Evaluate side-chains 675 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 590 time to evaluate : 4.501 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 69 residues processed: 17 average time/residue: 1.0433 time to fit residues: 32.0424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 382 optimal weight: 7.9990 chunk 247 optimal weight: 4.9990 chunk 369 optimal weight: 0.4980 chunk 186 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 393 optimal weight: 0.6980 chunk 421 optimal weight: 4.9990 chunk 305 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 486 optimal weight: 3.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 73 ASN U 28 ASN ** g 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 9 GLN I 168 GLN J 154 GLN O 103 ASN V 49 GLN e 44 ASN 1 160 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 79399 Z= 0.285 Angle : 0.653 11.260 115134 Z= 0.338 Chirality : 0.043 0.307 14211 Planarity : 0.005 0.096 8425 Dihedral : 15.337 179.262 25375 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.08 % Favored : 95.90 % Rotamer Outliers : 2.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.54 (0.12), residues: 4809 helix: 0.16 (0.13), residues: 1489 sheet: 0.11 (0.17), residues: 888 loop : -0.81 (0.12), residues: 2432 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 590 time to evaluate : 4.618 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 85 residues processed: 673 average time/residue: 1.7795 time to fit residues: 1551.1304 Evaluate side-chains 669 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 584 time to evaluate : 4.496 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 72 residues processed: 14 average time/residue: 0.7723 time to fit residues: 23.5634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 562 optimal weight: 4.9990 chunk 592 optimal weight: 0.9990 chunk 540 optimal weight: 4.9990 chunk 576 optimal weight: 2.9990 chunk 347 optimal weight: 0.9980 chunk 251 optimal weight: 0.7980 chunk 452 optimal weight: 6.9990 chunk 176 optimal weight: 6.9990 chunk 521 optimal weight: 4.9990 chunk 545 optimal weight: 10.0000 chunk 574 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 73 ASN U 28 ASN ** g 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 181 ASN A 9 GLN H 97 GLN I 168 GLN J 154 GLN O 103 ASN V 49 GLN 1 160 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 79399 Z= 0.201 Angle : 0.609 11.057 115134 Z= 0.317 Chirality : 0.040 0.289 14211 Planarity : 0.005 0.096 8425 Dihedral : 15.314 179.119 25375 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.85 % Favored : 96.13 % Rotamer Outliers : 2.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.43 (0.12), residues: 4809 helix: 0.30 (0.14), residues: 1488 sheet: 0.16 (0.17), residues: 889 loop : -0.77 (0.12), residues: 2432 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 587 time to evaluate : 4.628 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 109 outliers final: 78 residues processed: 666 average time/residue: 1.7795 time to fit residues: 1542.4271 Evaluate side-chains 660 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 582 time to evaluate : 4.608 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 71 residues processed: 9 average time/residue: 0.9666 time to fit residues: 19.4098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 378 optimal weight: 1.9990 chunk 609 optimal weight: 7.9990 chunk 372 optimal weight: 3.9990 chunk 289 optimal weight: 2.9990 chunk 423 optimal weight: 4.9990 chunk 639 optimal weight: 1.9990 chunk 588 optimal weight: 4.9990 chunk 509 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 393 optimal weight: 0.5980 chunk 312 optimal weight: 10.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 73 ASN U 28 ASN ** g 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 9 GLN I 168 GLN J 154 GLN O 103 ASN V 49 GLN 1 160 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 79399 Z= 0.242 Angle : 0.623 10.868 115134 Z= 0.323 Chirality : 0.041 0.297 14211 Planarity : 0.005 0.097 8425 Dihedral : 15.285 179.079 25375 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.05 % Favored : 95.92 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.45 (0.12), residues: 4809 helix: 0.28 (0.14), residues: 1487 sheet: 0.14 (0.17), residues: 891 loop : -0.78 (0.12), residues: 2431 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 583 time to evaluate : 4.595 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 77 residues processed: 656 average time/residue: 1.8600 time to fit residues: 1581.8636 Evaluate side-chains 655 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 578 time to evaluate : 4.589 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 73 residues processed: 5 average time/residue: 0.6136 time to fit residues: 11.4536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 404 optimal weight: 6.9990 chunk 542 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 469 optimal weight: 0.9980 chunk 75 optimal weight: 20.0000 chunk 141 optimal weight: 7.9990 chunk 510 optimal weight: 2.9990 chunk 213 optimal weight: 0.5980 chunk 523 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 73 ASN U 28 ASN ** g 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 181 ASN A 9 GLN H 97 GLN I 168 GLN J 154 GLN O 103 ASN V 49 GLN 1 160 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.158058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.139352 restraints weight = 80416.745| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 0.82 r_work: 0.3305 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.070 79399 Z= 0.343 Angle : 0.702 11.947 115134 Z= 0.361 Chirality : 0.045 0.321 14211 Planarity : 0.006 0.097 8425 Dihedral : 15.419 179.079 25375 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.37 % Favored : 95.61 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.63 (0.12), residues: 4809 helix: 0.11 (0.13), residues: 1483 sheet: 0.05 (0.17), residues: 886 loop : -0.87 (0.12), residues: 2440 =============================================================================== Job complete usr+sys time: 21665.20 seconds wall clock time: 378 minutes 54.92 seconds (22734.92 seconds total)