Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 17 02:59:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aqd_11864/07_2023/7aqd_11864.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aqd_11864/07_2023/7aqd_11864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aqd_11864/07_2023/7aqd_11864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aqd_11864/07_2023/7aqd_11864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aqd_11864/07_2023/7aqd_11864.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aqd_11864/07_2023/7aqd_11864.pdb" } resolution = 3.1 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= 0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 3106 5.49 5 S 97 5.16 5 C 47093 2.51 5 N 17514 2.21 5 O 26547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ASP 4": "OD1" <-> "OD2" Residue "R GLU 14": "OE1" <-> "OE2" Residue "R ARG 40": "NH1" <-> "NH2" Residue "R GLU 71": "OE1" <-> "OE2" Residue "R PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 125": "NH1" <-> "NH2" Residue "R GLU 136": "OE1" <-> "OE2" Residue "R ARG 191": "NH1" <-> "NH2" Residue "R ARG 238": "NH1" <-> "NH2" Residue "R GLU 256": "OE1" <-> "OE2" Residue "R PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 284": "NH1" <-> "NH2" Residue "R TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 343": "OD1" <-> "OD2" Residue "R GLU 347": "OE1" <-> "OE2" Residue "R TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 354": "OE1" <-> "OE2" Residue "R GLU 392": "OE1" <-> "OE2" Residue "R GLU 399": "OE1" <-> "OE2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C GLU 115": "OE1" <-> "OE2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C GLU 198": "OE1" <-> "OE2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "D GLU 18": "OE1" <-> "OE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D GLU 65": "OE1" <-> "OE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "F GLU 11": "OE1" <-> "OE2" Residue "F GLU 32": "OE1" <-> "OE2" Residue "F ARG 80": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F GLU 168": "OE1" <-> "OE2" Residue "G ARG 96": "NH1" <-> "NH2" Residue "G GLU 115": "OE1" <-> "OE2" Residue "G GLU 119": "OE1" <-> "OE2" Residue "G GLU 140": "OE1" <-> "OE2" Residue "G ARG 172": "NH1" <-> "NH2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "I GLU 91": "OE1" <-> "OE2" Residue "I GLU 107": "OE1" <-> "OE2" Residue "I GLU 110": "OE1" <-> "OE2" Residue "I GLU 122": "OE1" <-> "OE2" Residue "J GLU 13": "OE1" <-> "OE2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "J GLU 99": "OE1" <-> "OE2" Residue "J GLU 130": "OE1" <-> "OE2" Residue "K GLU 5": "OE1" <-> "OE2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K GLU 108": "OE1" <-> "OE2" Residue "L GLU 5": "OE1" <-> "OE2" Residue "L GLU 73": "OE1" <-> "OE2" Residue "L GLU 90": "OE1" <-> "OE2" Residue "L GLU 94": "OE1" <-> "OE2" Residue "L GLU 98": "OE1" <-> "OE2" Residue "L GLU 118": "OE1" <-> "OE2" Residue "L GLU 137": "OE1" <-> "OE2" Residue "L GLU 144": "OE1" <-> "OE2" Residue "M GLU 38": "OE1" <-> "OE2" Residue "M GLU 48": "OE1" <-> "OE2" Residue "M GLU 80": "OE1" <-> "OE2" Residue "M GLU 135": "OE1" <-> "OE2" Residue "M GLU 136": "OE1" <-> "OE2" Residue "N GLU 28": "OE1" <-> "OE2" Residue "N GLU 31": "OE1" <-> "OE2" Residue "N GLU 39": "OE1" <-> "OE2" Residue "N GLU 69": "OE1" <-> "OE2" Residue "N GLU 73": "OE1" <-> "OE2" Residue "O ARG 11": "NH1" <-> "NH2" Residue "O GLU 66": "OE1" <-> "OE2" Residue "O GLU 115": "OE1" <-> "OE2" Residue "Q PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 31": "OE1" <-> "OE2" Residue "S GLU 48": "OE1" <-> "OE2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 86": "NH1" <-> "NH2" Residue "U GLU 86": "OE1" <-> "OE2" Residue "V ARG 28": "NH1" <-> "NH2" Residue "Z GLU 5": "OE1" <-> "OE2" Residue "Z GLU 38": "OE1" <-> "OE2" Residue "Z GLU 58": "OE1" <-> "OE2" Residue "a GLU 41": "OE1" <-> "OE2" Residue "a ARG 42": "NH1" <-> "NH2" Residue "a GLU 60": "OE1" <-> "OE2" Residue "a GLU 115": "OE1" <-> "OE2" Residue "b GLU 29": "OE1" <-> "OE2" Residue "f GLU 28": "OE1" <-> "OE2" Residue "g GLU 15": "OE1" <-> "OE2" Residue "g GLU 16": "OE1" <-> "OE2" Residue "g GLU 23": "OE1" <-> "OE2" Residue "g GLU 28": "OE1" <-> "OE2" Residue "g GLU 54": "OE1" <-> "OE2" Residue "g ARG 89": "NH1" <-> "NH2" Residue "h GLU 44": "OE1" <-> "OE2" Residue "h ARG 75": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 94357 Number of models: 1 Model: "" Number of chains: 32 Chain: "R" Number of atoms: 3519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3519 Classifications: {'peptide': 433} Link IDs: {'CIS': 4, 'PTRANS': 19, 'TRANS': 409} Chain: "A" Number of atoms: 62663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2918, 62663 Classifications: {'RNA': 2918} Modifications used: {'rna2p_pur': 277, 'rna2p_pyr': 151, 'rna3p_pur': 1416, 'rna3p_pyr': 1074} Link IDs: {'rna2p': 428, 'rna3p': 2489} Chain breaks: 1 Chain: "B" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2395 Classifications: {'RNA': 112} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 9, 'rna3p_pur': 53, 'rna3p_pyr': 43} Link IDs: {'rna2p': 16, 'rna3p': 95} Chain: "C" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2111 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 17, 'TRANS': 257} Chain: "D" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1575 Classifications: {'peptide': 207} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 193} Chain: "E" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1561 Classifications: {'peptide': 205} Link IDs: {'CIS': 3, 'PTRANS': 7, 'TRANS': 194} Chain: "F" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1404 Classifications: {'peptide': 178} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 168} Chain: "G" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 164} Chain: "I" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 981 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 10, 'TRANS': 122} Chain: "J" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1123 Classifications: {'peptide': 142} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 131} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 920 Classifications: {'peptide': 122} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 116} Chain: "L" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1081 Classifications: {'peptide': 146} Link IDs: {'CIS': 4, 'PTRANS': 5, 'TRANS': 136} Chain: "M" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1097 Classifications: {'peptide': 138} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain: "N" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 953 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "O" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 912 Classifications: {'peptide': 120} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 115} Chain: "Q" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 940 Classifications: {'peptide': 117} Link IDs: {'CIS': 1, 'TRANS': 115} Chain: "S" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 103} Chain: "T" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1622 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 7, 'rna3p_pur': 28, 'rna3p_pyr': 31} Link IDs: {'rna2p': 16, 'rna3p': 59} Chain: "U" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 754 Classifications: {'peptide': 100} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 91} Chain: "V" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 630 Classifications: {'peptide': 82} Link IDs: {'CIS': 2, 'PTRANS': 2, 'TRANS': 77} Chain: "W" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 35 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "X" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'CIS': 4, 'PTRANS': 1, 'TRANS': 52} Chain: "Z" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "a" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 936 Classifications: {'peptide': 114} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 107} Chain: "b" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'CIS': 3, 'PTRANS': 3, 'TRANS': 47} Chain: "c" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 401 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "d" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 367 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "e" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 512 Classifications: {'peptide': 64} Link IDs: {'CIS': 2, 'TRANS': 61} Chain: "f" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 288 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "g" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 786 Classifications: {'peptide': 101} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 96} Chain: "h" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 752 Classifications: {'peptide': 93} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 89} Chain: "i" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Time building chain proxies: 33.01, per 1000 atoms: 0.35 Number of scatterers: 94357 At special positions: 0 Unit cell: (208.65, 201.16, 225.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 97 16.00 P 3106 15.00 O 26547 8.00 N 17514 7.00 C 47093 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 86133 O4' U T 34 .*. O " rejected from bonding due to valence issues. Atom "ATOM 86176 O4' C T 36 .*. O " rejected from bonding due to valence issues. Atom "ATOM 86281 O4' A T 41 .*. O " rejected from bonding due to valence issues. Atom "ATOM 86281 O4' A T 41 .*. O " rejected from bonding due to valence issues. Atom "ATOM 86218 O4' C T 38 .*. O " rejected from bonding due to valence issues. Atom "ATOM 86150 O5' G T 35 .*. O " rejected from bonding due to valence issues. Atom "ATOM 61097 O5' A A2689 .*. O " rejected from bonding due to valence issues. Atom "ATOM 86133 O4' U T 34 .*. O " rejected from bonding due to valence issues. Atom "ATOM 86130 O5' U T 34 .*. O " rejected from bonding due to valence issues. Atom "ATOM 61097 O5' A A2689 .*. O " rejected from bonding due to valence issues. Atom "ATOM 61097 O5' A A2689 .*. O " rejected from bonding due to valence issues. Atom "ATOM 86130 O5' U T 34 .*. O " rejected from bonding due to valence issues. Atom "ATOM 86047 O5' G T 30 .*. O " rejected from bonding due to valence issues. Atom "ATOM 86218 O4' C T 38 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 35.58 Conformation dependent library (CDL) restraints added in 3.4 seconds 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6474 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 52 sheets defined 30.3% alpha, 18.6% beta 1030 base pairs and 1710 stacking pairs defined. Time for finding SS restraints: 31.19 Creating SS restraints... Processing helix chain 'R' and resid 4 through 19 Processing helix chain 'R' and resid 73 through 83 Processing helix chain 'R' and resid 123 through 127 removed outlier: 3.522A pdb=" N HIS R 126 " --> pdb=" O MET R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 200 Processing helix chain 'R' and resid 204 through 215 Processing helix chain 'R' and resid 223 through 235 Processing helix chain 'R' and resid 236 through 238 No H-bonds generated for 'chain 'R' and resid 236 through 238' Processing helix chain 'R' and resid 269 through 277 Processing helix chain 'R' and resid 281 through 335 removed outlier: 4.184A pdb=" N GLN R 292 " --> pdb=" O LYS R 288 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASP R 293 " --> pdb=" O GLN R 289 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU R 320 " --> pdb=" O LEU R 316 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA R 334 " --> pdb=" O GLU R 330 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 368 through 413 removed outlier: 4.124A pdb=" N ALA R 373 " --> pdb=" O PRO R 369 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU R 391 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER R 413 " --> pdb=" O GLN R 409 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 430 Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 197 through 203 removed outlier: 4.386A pdb=" N GLU C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 removed outlier: 3.648A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 removed outlier: 3.661A pdb=" N VAL C 224 " --> pdb=" O ARG C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 removed outlier: 4.262A pdb=" N LYS C 268 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 69 Processing helix chain 'D' and resid 98 through 102 removed outlier: 3.717A pdb=" N ILE D 101 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 127 Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 29 through 42 Processing helix chain 'E' and resid 102 through 120 Processing helix chain 'E' and resid 135 through 146 removed outlier: 3.998A pdb=" N MET E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 166 Processing helix chain 'E' and resid 182 through 190 removed outlier: 3.695A pdb=" N VAL E 186 " --> pdb=" O ASN E 182 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU E 190 " --> pdb=" O VAL E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 4.619A pdb=" N GLU E 204 " --> pdb=" O GLU E 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 20 removed outlier: 3.799A pdb=" N ASN F 9 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ALA F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) Proline residue: F 14 - end of helix removed outlier: 3.925A pdb=" N MET F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE F 20 " --> pdb=" O LEU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 57 removed outlier: 3.967A pdb=" N LEU F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 111 removed outlier: 3.992A pdb=" N LYS F 102 " --> pdb=" O ASP F 98 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 162 through 173 removed outlier: 3.730A pdb=" N GLU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN F 172 " --> pdb=" O GLU F 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 82 removed outlier: 3.853A pdb=" N GLY G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER G 81 " --> pdb=" O VAL G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 153 removed outlier: 3.938A pdb=" N VAL G 152 " --> pdb=" O ASN G 148 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG G 153 " --> pdb=" O ILE G 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 30 removed outlier: 3.954A pdb=" N ALA I 27 " --> pdb=" O PRO I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 46 removed outlier: 4.257A pdb=" N LYS I 40 " --> pdb=" O MET I 36 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLU I 41 " --> pdb=" O GLY I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 84 Processing helix chain 'I' and resid 102 through 112 removed outlier: 3.656A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 135 Processing helix chain 'J' and resid 27 through 39 removed outlier: 3.892A pdb=" N SER J 31 " --> pdb=" O GLY J 27 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU J 32 " --> pdb=" O ARG J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 63 removed outlier: 3.528A pdb=" N ILE J 63 " --> pdb=" O ALA J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 73 Processing helix chain 'J' and resid 90 through 97 removed outlier: 3.577A pdb=" N TYR J 97 " --> pdb=" O MET J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 110 Processing helix chain 'J' and resid 113 through 121 removed outlier: 3.560A pdb=" N LYS J 121 " --> pdb=" O ARG J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 137 Processing helix chain 'K' and resid 105 through 107 No H-bonds generated for 'chain 'K' and resid 105 through 107' Processing helix chain 'K' and resid 111 through 118 Processing helix chain 'L' and resid 56 through 61 Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.583A pdb=" N GLY L 84 " --> pdb=" O LYS L 81 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE L 85 " --> pdb=" O LEU L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 100 removed outlier: 3.905A pdb=" N GLU L 98 " --> pdb=" O GLU L 94 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY L 100 " --> pdb=" O LEU L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 139 Processing helix chain 'M' and resid 44 through 58 removed outlier: 3.857A pdb=" N TYR M 57 " --> pdb=" O ALA M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 123 Processing helix chain 'N' and resid 9 through 28 Processing helix chain 'N' and resid 34 through 54 removed outlier: 4.386A pdb=" N SER N 42 " --> pdb=" O LYS N 38 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL N 43 " --> pdb=" O GLU N 39 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG N 53 " --> pdb=" O THR N 49 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY N 54 " --> pdb=" O LEU N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 64 removed outlier: 3.601A pdb=" N ALA N 64 " --> pdb=" O ARG N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 86 removed outlier: 3.672A pdb=" N PHE N 84 " --> pdb=" O LEU N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 91 Processing helix chain 'O' and resid 6 through 22 removed outlier: 3.605A pdb=" N ALA O 10 " --> pdb=" O SER O 6 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS O 13 " --> pdb=" O ALA O 9 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS O 21 " --> pdb=" O ARG O 17 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU O 22 " --> pdb=" O VAL O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 87 removed outlier: 4.367A pdb=" N VAL O 77 " --> pdb=" O ALA O 73 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA O 82 " --> pdb=" O GLY O 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 117 removed outlier: 3.636A pdb=" N GLY O 117 " --> pdb=" O ALA O 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 21 removed outlier: 4.145A pdb=" N ARG Q 11 " --> pdb=" O GLY Q 7 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 3.707A pdb=" N HIS Q 29 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 72 removed outlier: 4.214A pdb=" N GLN Q 37 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 86 Processing helix chain 'Q' and resid 92 through 99 Processing helix chain 'Q' and resid 104 through 116 removed outlier: 3.964A pdb=" N GLN Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.620A pdb=" N LEU S 19 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 31 Processing helix chain 'S' and resid 32 through 38 removed outlier: 3.768A pdb=" N LEU S 38 " --> pdb=" O SER S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 61 Processing helix chain 'S' and resid 65 through 67 No H-bonds generated for 'chain 'S' and resid 65 through 67' Processing helix chain 'Z' and resid 16 through 26 Processing helix chain 'Z' and resid 40 through 50 removed outlier: 3.541A pdb=" N MET Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 13 Processing helix chain 'a' and resid 56 through 59 Processing helix chain 'a' and resid 100 through 105 removed outlier: 3.802A pdb=" N ARG a 104 " --> pdb=" O TYR a 101 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU a 105 " --> pdb=" O TYR a 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 108 through 113 removed outlier: 3.600A pdb=" N ARG a 112 " --> pdb=" O GLY a 108 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 17 Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 17 through 23 Processing helix chain 'd' and resid 24 through 38 Processing helix chain 'e' and resid 7 through 14 Processing helix chain 'e' and resid 37 through 45 removed outlier: 3.597A pdb=" N LYS e 43 " --> pdb=" O LYS e 39 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 59 removed outlier: 3.981A pdb=" N ARG e 57 " --> pdb=" O GLY e 53 " (cutoff:3.500A) Processing helix chain 'f' and resid 18 through 22 removed outlier: 3.719A pdb=" N GLY f 21 " --> pdb=" O ARG f 18 " (cutoff:3.500A) Processing helix chain 'f' and resid 29 through 33 removed outlier: 3.597A pdb=" N LYS f 33 " --> pdb=" O PRO f 30 " (cutoff:3.500A) Processing helix chain 'h' and resid 3 through 6 Processing helix chain 'h' and resid 14 through 21 Processing helix chain 'h' and resid 35 through 47 Processing helix chain 'i' and resid 2 through 8 Processing helix chain 'i' and resid 9 through 35 removed outlier: 3.749A pdb=" N GLU i 13 " --> pdb=" O LEU i 9 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL i 18 " --> pdb=" O ILE i 14 " (cutoff:3.500A) Processing helix chain 'i' and resid 39 through 65 Processing sheet with id=AA1, first strand: chain 'R' and resid 59 through 62 removed outlier: 4.286A pdb=" N LYS R 47 " --> pdb=" O THR R 62 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS R 26 " --> pdb=" O HIS R 38 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG R 40 " --> pdb=" O ILE R 24 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ILE R 24 " --> pdb=" O ARG R 40 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N HIS R 103 " --> pdb=" O GLU R 89 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE R 91 " --> pdb=" O ILE R 101 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE R 101 " --> pdb=" O ILE R 91 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLN R 93 " --> pdb=" O ILE R 99 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ILE R 99 " --> pdb=" O GLN R 93 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER R 106 " --> pdb=" O THR R 114 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE R 129 " --> pdb=" O GLY R 142 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY R 142 " --> pdb=" O ILE R 129 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU R 131 " --> pdb=" O ILE R 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 242 through 245 removed outlier: 3.559A pdb=" N TYR R 253 " --> pdb=" O ASN R 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA4, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.767A pdb=" N THR C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN C 95 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL C 78 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 129 through 131 Processing sheet with id=AA7, first strand: chain 'C' and resid 163 through 167 removed outlier: 6.353A pdb=" N LEU C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LYS C 167 " --> pdb=" O TYR C 171 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TYR C 171 " --> pdb=" O LYS C 167 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N MET C 183 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE C 270 " --> pdb=" O MET C 183 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 4 through 16 removed outlier: 6.927A pdb=" N VAL D 27 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N MET D 12 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL D 25 " --> pdb=" O MET D 12 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLN D 14 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE D 23 " --> pdb=" O GLN D 14 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU D 185 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL D 179 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU D 187 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU D 175 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL D 108 " --> pdb=" O ASN D 173 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL D 113 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU D 199 " --> pdb=" O VAL D 113 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 77 through 83 removed outlier: 6.545A pdb=" N LYS D 77 " --> pdb=" O ASP D 55 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASP D 55 " --> pdb=" O LYS D 77 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLY D 52 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL D 35 " --> pdb=" O GLY D 52 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N ASP D 54 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 10.028A pdb=" N ASN D 33 " --> pdb=" O ASP D 54 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 118 through 120 removed outlier: 3.609A pdb=" N GLY D 118 " --> pdb=" O MET D 164 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 16 through 18 removed outlier: 3.881A pdb=" N VAL E 4 " --> pdb=" O ILE E 17 " (cutoff:3.500A) removed outlier: 9.377A pdb=" N ILE E 123 " --> pdb=" O LYS E 3 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA E 5 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N VAL E 125 " --> pdb=" O ALA E 5 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE E 124 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ALA E 152 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL E 176 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE E 154 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 66 through 67 removed outlier: 3.504A pdb=" N VAL F 66 " --> pdb=" O LYS F 88 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU F 91 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE F 34 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL F 157 " --> pdb=" O GLU F 32 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE F 34 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL F 155 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE F 36 " --> pdb=" O ASP F 153 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP F 153 " --> pdb=" O ILE F 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 9 through 10 removed outlier: 3.954A pdb=" N LEU G 9 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL G 50 " --> pdb=" O GLU G 47 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR G 52 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS G 45 " --> pdb=" O THR G 52 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 16 through 17 removed outlier: 3.570A pdb=" N THR G 16 " --> pdb=" O LYS G 28 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU G 34 " --> pdb=" O VAL G 27 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY G 29 " --> pdb=" O GLY G 32 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY G 32 " --> pdb=" O GLY G 29 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 123 through 125 removed outlier: 3.728A pdb=" N VAL G 134 " --> pdb=" O ARG G 86 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG G 86 " --> pdb=" O VAL G 134 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY G 136 " --> pdb=" O PHE G 84 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY G 162 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 97 through 100 removed outlier: 3.724A pdb=" N LEU G 104 " --> pdb=" O ILE G 116 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 9 through 14 removed outlier: 3.683A pdb=" N VAL I 9 " --> pdb=" O ILE I 58 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE I 58 " --> pdb=" O VAL I 9 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU I 11 " --> pdb=" O VAL I 56 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 98 through 101 removed outlier: 6.979A pdb=" N ALA I 98 " --> pdb=" O VAL I 138 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLU I 140 " --> pdb=" O ALA I 98 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL I 100 " --> pdb=" O GLU I 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'J' and resid 123 through 125 removed outlier: 6.480A pdb=" N TRP J 16 " --> pdb=" O GLU J 139 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 74 through 76 Processing sheet with id=AC3, first strand: chain 'K' and resid 7 through 10 removed outlier: 5.607A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA K 16 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA K 46 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N VAL K 24 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS K 59 " --> pdb=" O ILE K 87 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N CYS K 84 " --> pdb=" O ARG K 7 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ILE K 86 " --> pdb=" O LYS K 9 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 69 through 70 removed outlier: 6.724A pdb=" N THR a 61 " --> pdb=" O ARG a 53 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG a 53 " --> pdb=" O THR a 61 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR a 63 " --> pdb=" O ILE a 51 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ILE a 67 " --> pdb=" O GLU a 47 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N GLU a 47 " --> pdb=" O ILE a 67 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N THR a 28 " --> pdb=" O VAL a 89 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N VAL a 89 " --> pdb=" O THR a 28 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ARG a 30 " --> pdb=" O ILE a 87 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ILE a 87 " --> pdb=" O ARG a 30 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N HIS a 32 " --> pdb=" O ALA a 85 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 102 through 103 removed outlier: 6.138A pdb=" N VAL K 102 " --> pdb=" O ILE K 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'L' and resid 110 through 111 Processing sheet with id=AC7, first strand: chain 'L' and resid 122 through 125 Processing sheet with id=AC8, first strand: chain 'M' and resid 64 through 66 removed outlier: 6.895A pdb=" N VAL M 102 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA M 36 " --> pdb=" O VAL M 102 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N PHE M 104 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE M 34 " --> pdb=" O PHE M 104 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 40 through 43 removed outlier: 3.655A pdb=" N SER M 40 " --> pdb=" O VAL M 97 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL M 97 " --> pdb=" O SER M 40 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA M 89 " --> pdb=" O ALA M 76 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR M 74 " --> pdb=" O GLU M 91 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N TRP M 93 " --> pdb=" O LYS M 72 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LYS M 72 " --> pdb=" O TRP M 93 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 29 through 33 removed outlier: 4.287A pdb=" N MET N 114 " --> pdb=" O LEU N 104 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 70 through 72 removed outlier: 6.859A pdb=" N GLN N 77 " --> pdb=" O ALA N 71 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 52 through 57 removed outlier: 4.242A pdb=" N ALA O 54 " --> pdb=" O ILE O 44 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE O 45 " --> pdb=" O ARG O 30 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG O 30 " --> pdb=" O ILE O 45 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU O 31 " --> pdb=" O ASP O 96 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 3 through 6 removed outlier: 6.629A pdb=" N VAL S 106 " --> pdb=" O SER S 72 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 3 through 6 Processing sheet with id=AD6, first strand: chain 'S' and resid 82 through 86 Processing sheet with id=AD7, first strand: chain 'U' and resid 63 through 64 removed outlier: 3.672A pdb=" N ALA U 25 " --> pdb=" O LEU U 34 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'U' and resid 43 through 44 Processing sheet with id=AD9, first strand: chain 'U' and resid 81 through 82 Processing sheet with id=AE1, first strand: chain 'V' and resid 30 through 31 removed outlier: 6.836A pdb=" N LEU V 67 " --> pdb=" O LEU V 45 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'V' and resid 38 through 39 Processing sheet with id=AE3, first strand: chain 'X' and resid 13 through 17 removed outlier: 3.954A pdb=" N SER X 25 " --> pdb=" O ASN X 17 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'X' and resid 33 through 34 Processing sheet with id=AE5, first strand: chain 'Z' and resid 34 through 38 removed outlier: 3.677A pdb=" N LYS Z 57 " --> pdb=" O GLU Z 5 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR Z 7 " --> pdb=" O SER Z 55 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'a' and resid 93 through 94 removed outlier: 4.625A pdb=" N ILE a 116 " --> pdb=" O LYS a 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'b' and resid 27 through 28 Processing sheet with id=AE8, first strand: chain 'b' and resid 48 through 49 removed outlier: 3.607A pdb=" N LYS b 52 " --> pdb=" O TYR b 49 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'c' and resid 15 through 22 removed outlier: 6.632A pdb=" N ARG c 15 " --> pdb=" O CYS c 9 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N CYS c 9 " --> pdb=" O ARG c 15 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS c 21 " --> pdb=" O VAL c 3 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL c 3 " --> pdb=" O LYS c 21 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS c 41 " --> pdb=" O CYS c 36 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE c 32 " --> pdb=" O HIS c 45 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'e' and resid 23 through 25 Processing sheet with id=AF2, first strand: chain 'f' and resid 15 through 17 Processing sheet with id=AF3, first strand: chain 'g' and resid 3 through 6 removed outlier: 3.586A pdb=" N ALA g 3 " --> pdb=" O VAL g 14 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL g 14 " --> pdb=" O ALA g 3 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'g' and resid 18 through 23 removed outlier: 3.888A pdb=" N GLN g 18 " --> pdb=" O ILE g 97 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE g 97 " --> pdb=" O GLN g 18 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR g 92 " --> pdb=" O GLN g 65 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N GLN g 65 " --> pdb=" O TYR g 92 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LYS g 94 " --> pdb=" O GLU g 63 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR g 59 " --> pdb=" O GLU g 98 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'g' and resid 71 through 76 Processing sheet with id=AF6, first strand: chain 'h' and resid 8 through 11 removed outlier: 3.816A pdb=" N ARG h 10 " --> pdb=" O GLU h 29 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG h 77 " --> pdb=" O VAL h 30 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'h' and resid 63 through 66 970 hydrogen bonds defined for protein. 2727 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2625 hydrogen bonds 4238 hydrogen bond angles 0 basepair planarities 1030 basepair parallelities 1710 stacking parallelities Total time for adding SS restraints: 154.48 Time building geometry restraints manager: 38.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.23: 672 1.23 - 1.38: 34009 1.38 - 1.54: 61223 1.54 - 1.70: 6654 1.70 - 1.86: 180 Bond restraints: 102738 Sorted by residual: bond pdb=" C GLY R 429 " pdb=" N LYS R 430 " ideal model delta sigma weight residual 1.331 1.651 -0.320 1.29e-02 6.01e+03 6.17e+02 bond pdb=" CA LYS R 430 " pdb=" CB LYS R 430 " ideal model delta sigma weight residual 1.533 1.856 -0.323 1.72e-02 3.38e+03 3.52e+02 bond pdb=" C TYR R 431 " pdb=" N LEU R 432 " ideal model delta sigma weight residual 1.332 1.520 -0.187 1.40e-02 5.10e+03 1.79e+02 bond pdb=" C TYR R 431 " pdb=" O TYR R 431 " ideal model delta sigma weight residual 1.235 1.070 0.165 1.26e-02 6.30e+03 1.71e+02 bond pdb=" C SER R 412 " pdb=" N SER R 413 " ideal model delta sigma weight residual 1.332 1.510 -0.178 1.40e-02 5.10e+03 1.62e+02 ... (remaining 102733 not shown) Histogram of bond angle deviations from ideal: 32.02 - 58.02: 4 58.02 - 84.02: 11 84.02 - 110.03: 48114 110.03 - 136.03: 105950 136.03 - 162.03: 9 Bond angle restraints: 154088 Sorted by residual: angle pdb=" CD1 TYR R 431 " pdb=" CG TYR R 431 " pdb=" CD2 TYR R 431 " ideal model delta sigma weight residual 118.10 32.02 86.08 1.50e+00 4.44e-01 3.29e+03 angle pdb=" CD1 PHE R 3 " pdb=" CE1 PHE R 3 " pdb=" CZ PHE R 3 " ideal model delta sigma weight residual 120.00 34.63 85.37 1.80e+00 3.09e-01 2.25e+03 angle pdb=" N LYS R 430 " pdb=" CA LYS R 430 " pdb=" CB LYS R 430 " ideal model delta sigma weight residual 111.13 40.35 70.78 1.81e+00 3.05e-01 1.53e+03 angle pdb=" CG TYR R 431 " pdb=" CD2 TYR R 431 " pdb=" CE2 TYR R 431 " ideal model delta sigma weight residual 121.20 64.12 57.08 1.50e+00 4.44e-01 1.45e+03 angle pdb=" CG TYR R 431 " pdb=" CD1 TYR R 431 " pdb=" CE1 TYR R 431 " ideal model delta sigma weight residual 121.20 64.43 56.77 1.50e+00 4.44e-01 1.43e+03 ... (remaining 154083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 52178 35.99 - 71.97: 2353 71.97 - 107.96: 158 107.96 - 143.95: 31 143.95 - 179.94: 47 Dihedral angle restraints: 54767 sinusoidal: 44695 harmonic: 10072 Sorted by residual: dihedral pdb=" N LYS R 430 " pdb=" C LYS R 430 " pdb=" CA LYS R 430 " pdb=" CB LYS R 430 " ideal model delta harmonic sigma weight residual 122.80 34.38 88.42 0 2.50e+00 1.60e-01 1.25e+03 dihedral pdb=" CA SER R 2 " pdb=" C SER R 2 " pdb=" N PHE R 3 " pdb=" CA PHE R 3 " ideal model delta harmonic sigma weight residual -180.00 -55.50 -124.50 0 5.00e+00 4.00e-02 6.20e+02 dihedral pdb=" CA PHE R 279 " pdb=" C PHE R 279 " pdb=" N GLY R 280 " pdb=" CA GLY R 280 " ideal model delta harmonic sigma weight residual -180.00 -67.46 -112.54 0 5.00e+00 4.00e-02 5.07e+02 ... (remaining 54764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.349: 19713 0.349 - 0.699: 13 0.699 - 1.048: 1 1.048 - 1.398: 1 1.398 - 1.747: 1 Chirality restraints: 19729 Sorted by residual: chirality pdb=" CA ASP R 4 " pdb=" N ASP R 4 " pdb=" C ASP R 4 " pdb=" CB ASP R 4 " both_signs ideal model delta sigma weight residual False 2.51 0.76 1.75 2.00e-01 2.50e+01 7.63e+01 chirality pdb=" C3' C T 74 " pdb=" C4' C T 74 " pdb=" O3' C T 74 " pdb=" C2' C T 74 " both_signs ideal model delta sigma weight residual False -2.48 -1.27 -1.21 2.00e-01 2.50e+01 3.65e+01 chirality pdb=" CA PHE R 3 " pdb=" N PHE R 3 " pdb=" C PHE R 3 " pdb=" CB PHE R 3 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.77 2.00e-01 2.50e+01 1.46e+01 ... (remaining 19726 not shown) Planarity restraints: 7951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 431 " 0.034 2.00e-02 2.50e+03 4.36e-01 3.80e+03 pdb=" CG TYR R 431 " -0.104 2.00e-02 2.50e+03 pdb=" CD1 TYR R 431 " 0.168 2.00e-02 2.50e+03 pdb=" CD2 TYR R 431 " -0.256 2.00e-02 2.50e+03 pdb=" CE1 TYR R 431 " 0.777 2.00e-02 2.50e+03 pdb=" CE2 TYR R 431 " -0.880 2.00e-02 2.50e+03 pdb=" CZ TYR R 431 " 0.159 2.00e-02 2.50e+03 pdb=" OH TYR R 431 " 0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 3 " 0.124 2.00e-02 2.50e+03 2.80e-01 1.37e+03 pdb=" CG PHE R 3 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE R 3 " 0.112 2.00e-02 2.50e+03 pdb=" CD2 PHE R 3 " 0.262 2.00e-02 2.50e+03 pdb=" CE1 PHE R 3 " -0.498 2.00e-02 2.50e+03 pdb=" CE2 PHE R 3 " 0.317 2.00e-02 2.50e+03 pdb=" CZ PHE R 3 " -0.321 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C T 72 " 0.373 2.00e-02 2.50e+03 1.83e-01 7.53e+02 pdb=" N1 C T 72 " -0.070 2.00e-02 2.50e+03 pdb=" C2 C T 72 " -0.092 2.00e-02 2.50e+03 pdb=" O2 C T 72 " -0.139 2.00e-02 2.50e+03 pdb=" N3 C T 72 " -0.012 2.00e-02 2.50e+03 pdb=" C4 C T 72 " 0.019 2.00e-02 2.50e+03 pdb=" N4 C T 72 " 0.263 2.00e-02 2.50e+03 pdb=" C5 C T 72 " -0.141 2.00e-02 2.50e+03 pdb=" C6 C T 72 " -0.200 2.00e-02 2.50e+03 ... (remaining 7948 not shown) Histogram of nonbonded interaction distances: 0.15 - 1.10: 36 1.10 - 2.05: 176 2.05 - 3.00: 43734 3.00 - 3.95: 297172 3.95 - 4.90: 512077 Warning: very small nonbonded interaction distances. Nonbonded interactions: 853195 Sorted by model distance: nonbonded pdb=" CE LYS R 367 " pdb=" P A A2689 " model vdw 0.152 3.800 nonbonded pdb=" O TYR R 351 " pdb=" C GLY I 29 " model vdw 0.271 3.270 nonbonded pdb=" CB ARG R 125 " pdb=" O3' C T 38 " model vdw 0.357 3.440 nonbonded pdb=" N VAL R 203 " pdb=" N1 G T 35 " model vdw 0.412 3.200 nonbonded pdb=" CG MET R 123 " pdb=" N4 C T 38 " model vdw 0.418 3.520 ... (remaining 853190 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: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 17.180 Check model and map are aligned: 1.090 Set scattering table: 0.630 Process input model: 315.670 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.210 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 342.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 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 : 0.005 0.323 102738 Z= 0.287 Angle : 1.091 86.079 154088 Z= 0.601 Chirality : 0.047 1.747 19729 Planarity : 0.011 0.436 7951 Dihedral : 16.546 179.937 48293 Min Nonbonded Distance : 0.152 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.19 % Favored : 94.46 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 1.24 % Twisted Proline : 1.44 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.12), residues: 3485 helix: -1.77 (0.13), residues: 972 sheet: -0.16 (0.21), residues: 582 loop : -1.59 (0.12), residues: 1931 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1398 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1365 time to evaluate : 3.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 5 residues processed: 1394 average time/residue: 1.0064 time to fit residues: 2282.6605 Evaluate side-chains 999 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 994 time to evaluate : 3.979 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.9245 time to fit residues: 11.8895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 548 optimal weight: 0.7980 chunk 491 optimal weight: 0.8980 chunk 272 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 chunk 331 optimal weight: 10.0000 chunk 262 optimal weight: 60.0000 chunk 508 optimal weight: 0.4980 chunk 196 optimal weight: 10.0000 chunk 309 optimal weight: 8.9990 chunk 378 optimal weight: 10.0000 chunk 589 optimal weight: 9.9990 overall best weight: 4.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 366 ASN ** R 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 381 GLN C 226 ASN D 14 GLN D 33 ASN D 152 ASN E 122 ASN ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 GLN G 39 HIS I 43 ASN ** J 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 ASN e 64 ASN f 32 HIS ** f 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 81 ASN i 16 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.957 102738 Z= 0.417 Angle : 0.713 32.807 154088 Z= 0.372 Chirality : 0.040 1.163 19729 Planarity : 0.006 0.088 7951 Dihedral : 16.097 179.803 41149 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.42 % Favored : 94.35 % Rotamer Outliers : 4.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 1.24 % Twisted Proline : 1.44 % Twisted General : 0.21 % 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: -1.41 (0.13), residues: 3485 helix: -0.45 (0.15), residues: 993 sheet: -0.27 (0.21), residues: 578 loop : -1.41 (0.13), residues: 1914 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1146 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1016 time to evaluate : 3.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 130 outliers final: 78 residues processed: 1073 average time/residue: 0.9492 time to fit residues: 1721.6595 Evaluate side-chains 1018 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 940 time to evaluate : 3.884 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 78 outliers final: 1 residues processed: 78 average time/residue: 0.7301 time to fit residues: 111.0926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 327 optimal weight: 7.9990 chunk 182 optimal weight: 7.9990 chunk 490 optimal weight: 1.9990 chunk 401 optimal weight: 1.9990 chunk 162 optimal weight: 10.0000 chunk 590 optimal weight: 2.9990 chunk 637 optimal weight: 4.9990 chunk 525 optimal weight: 5.9990 chunk 585 optimal weight: 4.9990 chunk 201 optimal weight: 20.0000 chunk 473 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 300 ASN ** R 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 37 GLN D 168 GLN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 GLN N 27 ASN ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 HIS Q 91 ASN U 67 ASN c 45 HIS d 26 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.961 102738 Z= 0.352 Angle : 0.623 33.317 154088 Z= 0.325 Chirality : 0.035 0.467 19729 Planarity : 0.005 0.092 7951 Dihedral : 16.086 179.934 41149 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.37 % Favored : 94.52 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 1.24 % Twisted Proline : 0.72 % Twisted General : 0.18 % 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: -1.11 (0.13), residues: 3485 helix: 0.01 (0.16), residues: 993 sheet: -0.24 (0.21), residues: 578 loop : -1.31 (0.13), residues: 1914 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 995 time to evaluate : 4.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 35 residues processed: 1022 average time/residue: 0.9445 time to fit residues: 1633.3869 Evaluate side-chains 969 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 934 time to evaluate : 3.944 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 35 outliers final: 1 residues processed: 35 average time/residue: 0.8775 time to fit residues: 59.8213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 583 optimal weight: 6.9990 chunk 443 optimal weight: 9.9990 chunk 306 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 281 optimal weight: 8.9990 chunk 396 optimal weight: 10.0000 chunk 592 optimal weight: 4.9990 chunk 627 optimal weight: 9.9990 chunk 309 optimal weight: 8.9990 chunk 561 optimal weight: 30.0000 chunk 169 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 16 ASN R 103 HIS ** R 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 HIS D 95 GLN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 ASN J 131 HIS L 59 GLN ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 91 ASN Z 19 GLN ** g 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.951 102738 Z= 0.619 Angle : 0.846 33.571 154088 Z= 0.432 Chirality : 0.046 0.411 19729 Planarity : 0.006 0.084 7951 Dihedral : 16.676 179.191 41149 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.51 % Favored : 93.37 % Rotamer Outliers : 5.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 1.24 % Twisted Proline : 0.72 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.13), residues: 3485 helix: -0.06 (0.16), residues: 976 sheet: -0.56 (0.21), residues: 557 loop : -1.47 (0.13), residues: 1952 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1111 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 952 time to evaluate : 4.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 159 outliers final: 91 residues processed: 1017 average time/residue: 0.9494 time to fit residues: 1632.1592 Evaluate side-chains 971 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 880 time to evaluate : 3.971 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 91 outliers final: 1 residues processed: 91 average time/residue: 0.7036 time to fit residues: 127.3305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 522 optimal weight: 0.7980 chunk 356 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 467 optimal weight: 1.9990 chunk 258 optimal weight: 50.0000 chunk 535 optimal weight: 4.9990 chunk 433 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 320 optimal weight: 10.0000 chunk 563 optimal weight: 8.9990 chunk 158 optimal weight: 30.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 16 ASN R 372 ASN C 153 GLN C 163 GLN D 140 HIS D 168 GLN D 173 ASN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 GLN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN Q 91 ASN ** U 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 19 GLN a 15 GLN ** g 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.957 102738 Z= 0.466 Angle : 0.709 33.414 154088 Z= 0.366 Chirality : 0.040 0.342 19729 Planarity : 0.005 0.077 7951 Dihedral : 16.576 179.222 41149 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.14 % Favored : 93.77 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 1.24 % Twisted Proline : 0.72 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.13), residues: 3485 helix: 0.10 (0.16), residues: 973 sheet: -0.56 (0.21), residues: 581 loop : -1.46 (0.13), residues: 1931 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 995 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 921 time to evaluate : 4.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 38 residues processed: 957 average time/residue: 0.9930 time to fit residues: 1613.9046 Evaluate side-chains 924 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 886 time to evaluate : 3.907 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 38 outliers final: 1 residues processed: 38 average time/residue: 0.7501 time to fit residues: 56.9825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 211 optimal weight: 7.9990 chunk 564 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 368 optimal weight: 7.9990 chunk 154 optimal weight: 50.0000 chunk 627 optimal weight: 5.9990 chunk 521 optimal weight: 4.9990 chunk 290 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 329 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 33 HIS R 137 ASN D 33 ASN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 ASN ** J 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 GLN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 91 ASN ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 19 GLN a 15 GLN c 4 ASN ** c 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.959 102738 Z= 0.513 Angle : 0.745 33.286 154088 Z= 0.383 Chirality : 0.042 0.360 19729 Planarity : 0.005 0.075 7951 Dihedral : 16.658 179.778 41149 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.94 % Favored : 92.97 % Rotamer Outliers : 3.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 1.24 % Twisted Proline : 0.72 % Twisted General : 0.09 % 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: -1.39 (0.13), residues: 3485 helix: 0.07 (0.16), residues: 978 sheet: -0.71 (0.21), residues: 547 loop : -1.53 (0.13), residues: 1960 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1013 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 909 time to evaluate : 3.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 71 residues processed: 943 average time/residue: 0.9388 time to fit residues: 1497.4665 Evaluate side-chains 948 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 877 time to evaluate : 3.935 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 71 outliers final: 1 residues processed: 71 average time/residue: 0.7144 time to fit residues: 99.5448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 605 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 357 optimal weight: 10.0000 chunk 458 optimal weight: 8.9990 chunk 355 optimal weight: 3.9990 chunk 528 optimal weight: 0.0470 chunk 350 optimal weight: 2.9990 chunk 625 optimal weight: 8.9990 chunk 391 optimal weight: 0.5980 chunk 381 optimal weight: 1.9990 chunk 288 optimal weight: 5.9990 overall best weight: 1.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN ** J 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 ASN L 54 GLN L 59 GLN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 ASN O 49 ASN Q 91 ASN S 2 GLN ** V 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 19 GLN ** a 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 64 ASN g 11 GLN ** g 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.963 102738 Z= 0.325 Angle : 0.632 33.221 154088 Z= 0.326 Chirality : 0.035 0.291 19729 Planarity : 0.004 0.072 7951 Dihedral : 16.483 179.550 41149 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.85 % Favored : 94.09 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 1.24 % Twisted Proline : 0.72 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.13), residues: 3485 helix: 0.27 (0.16), residues: 972 sheet: -0.64 (0.21), residues: 562 loop : -1.39 (0.13), residues: 1951 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 920 time to evaluate : 4.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 25 residues processed: 939 average time/residue: 0.9521 time to fit residues: 1514.3572 Evaluate side-chains 905 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 880 time to evaluate : 4.117 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 25 outliers final: 1 residues processed: 25 average time/residue: 0.8341 time to fit residues: 42.5440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 386 optimal weight: 6.9990 chunk 249 optimal weight: 8.9990 chunk 373 optimal weight: 0.4980 chunk 188 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 397 optimal weight: 0.7980 chunk 426 optimal weight: 20.0000 chunk 309 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 491 optimal weight: 1.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 HIS L 59 GLN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 GLN Q 37 GLN S 2 GLN Z 19 GLN a 15 GLN ** c 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 81 ASN ** g 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 39 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.963 102738 Z= 0.396 Angle : 0.666 33.177 154088 Z= 0.343 Chirality : 0.037 0.316 19729 Planarity : 0.005 0.091 7951 Dihedral : 16.430 179.710 41149 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.80 % Favored : 93.11 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 1.24 % Twisted Proline : 0.72 % Twisted General : 0.06 % 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: -1.22 (0.13), residues: 3485 helix: 0.26 (0.16), residues: 978 sheet: -0.72 (0.21), residues: 586 loop : -1.42 (0.13), residues: 1921 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 890 time to evaluate : 4.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 32 residues processed: 911 average time/residue: 0.9457 time to fit residues: 1461.5382 Evaluate side-chains 907 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 875 time to evaluate : 3.994 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 32 outliers final: 1 residues processed: 32 average time/residue: 0.7278 time to fit residues: 48.0402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 569 optimal weight: 3.9990 chunk 599 optimal weight: 3.9990 chunk 546 optimal weight: 9.9990 chunk 582 optimal weight: 0.9990 chunk 350 optimal weight: 1.9990 chunk 253 optimal weight: 7.9990 chunk 457 optimal weight: 20.0000 chunk 178 optimal weight: 8.9990 chunk 526 optimal weight: 10.0000 chunk 551 optimal weight: 0.9980 chunk 580 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 GLN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 GLN N 27 ASN Q 37 GLN S 2 GLN ** V 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 ASN Z 19 GLN a 15 GLN c 4 ASN ** c 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 81 ASN i 39 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.966 102738 Z= 0.347 Angle : 0.640 33.104 154088 Z= 0.330 Chirality : 0.035 0.295 19729 Planarity : 0.004 0.070 7951 Dihedral : 16.404 179.990 41149 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.20 % Favored : 93.72 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 1.24 % Twisted Proline : 0.72 % Twisted General : 0.06 % 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: -1.20 (0.13), residues: 3485 helix: 0.20 (0.16), residues: 983 sheet: -0.73 (0.21), residues: 579 loop : -1.36 (0.13), residues: 1923 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 891 time to evaluate : 4.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 15 residues processed: 898 average time/residue: 0.9386 time to fit residues: 1428.4840 Evaluate side-chains 879 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 864 time to evaluate : 4.192 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.7898 time to fit residues: 25.5452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 382 optimal weight: 1.9990 chunk 616 optimal weight: 2.9990 chunk 376 optimal weight: 5.9990 chunk 292 optimal weight: 10.0000 chunk 428 optimal weight: 6.9990 chunk 646 optimal weight: 5.9990 chunk 595 optimal weight: 9.9990 chunk 514 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 397 optimal weight: 0.0570 chunk 315 optimal weight: 10.0000 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 GLN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 GLN Q 37 GLN S 2 GLN Z 19 GLN ** g 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 81 ASN ** g 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.965 102738 Z= 0.357 Angle : 0.646 33.130 154088 Z= 0.333 Chirality : 0.035 0.298 19729 Planarity : 0.004 0.070 7951 Dihedral : 16.348 179.955 41149 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.83 % Favored : 93.08 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 1.24 % Twisted Proline : 0.72 % Twisted General : 0.06 % 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: -1.17 (0.13), residues: 3485 helix: 0.24 (0.16), residues: 976 sheet: -0.70 (0.21), residues: 581 loop : -1.34 (0.13), residues: 1928 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 883 time to evaluate : 4.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 893 average time/residue: 0.9458 time to fit residues: 1431.4666 Evaluate side-chains 888 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 876 time to evaluate : 3.931 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.7236 time to fit residues: 20.5558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 408 optimal weight: 5.9990 chunk 548 optimal weight: 7.9990 chunk 157 optimal weight: 50.0000 chunk 474 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 515 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 529 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 398 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN L 59 GLN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 46 GLN ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN S 2 GLN U 44 HIS Z 19 GLN ** e 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 81 ASN ** g 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.104089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.065162 restraints weight = 250263.355| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.78 r_work: 0.2804 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.964 102738 Z= 0.518 Angle : 0.757 33.109 154088 Z= 0.386 Chirality : 0.042 0.364 19729 Planarity : 0.005 0.079 7951 Dihedral : 16.559 179.900 41149 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.49 % Favored : 92.45 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 1.24 % Twisted Proline : 0.72 % Twisted General : 0.06 % 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: -1.31 (0.13), residues: 3485 helix: 0.10 (0.16), residues: 981 sheet: -0.81 (0.21), residues: 568 loop : -1.41 (0.13), residues: 1936 =============================================================================== Job complete usr+sys time: 26019.16 seconds wall clock time: 456 minutes 40.27 seconds (27400.27 seconds total)