Starting phenix.real_space_refine on Tue Mar 19 15:33:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aqd_11864/03_2024/7aqd_11864.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aqd_11864/03_2024/7aqd_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_11864/03_2024/7aqd_11864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aqd_11864/03_2024/7aqd_11864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aqd_11864/03_2024/7aqd_11864.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aqd_11864/03_2024/7aqd_11864.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 37.47, per 1000 atoms: 0.40 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: 37.02 Conformation dependent library (CDL) restraints added in 4.6 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: 33.27 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: 159.44 Time building geometry restraints manager: 40.28 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: 57546 35.99 - 71.97: 7446 71.97 - 107.96: 825 107.96 - 143.95: 31 143.95 - 179.94: 47 Dihedral angle restraints: 65895 sinusoidal: 55823 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 65892 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: 3.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 14.670 Check model and map are aligned: 1.000 Set scattering table: 0.850 Process input model: 335.630 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.230 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:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 359.990 ------------------------------------------------------------------------------- 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 : 23.954 179.937 59421 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 % Allowed : 0.88 % Favored : 98.00 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP Q 61 HIS 0.010 0.001 HIS R 184 PHE 0.498 0.005 PHE R 3 TYR 0.880 0.006 TYR R 431 ARG 0.020 0.001 ARG G 96 *********************** 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 : 3.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 434 PRO cc_start: 0.3520 (OUTLIER) cc_final: 0.3319 (Cg_exo) REVERT: O 57 SER cc_start: 0.5591 (t) cc_final: 0.5327 (m) REVERT: c 12 CYS cc_start: 0.3028 (t) cc_final: 0.1632 (t) REVERT: h 74 SER cc_start: 0.8139 (t) cc_final: 0.7760 (m) outliers start: 33 outliers final: 5 residues processed: 1394 average time/residue: 1.0311 time to fit residues: 2340.8383 Evaluate side-chains 1001 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 995 time to evaluate : 3.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 3 PHE Chi-restraints excluded: chain R residue 263 GLU Chi-restraints excluded: chain R residue 336 LEU Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain R residue 417 ARG Chi-restraints excluded: chain R residue 434 PRO 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 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 366 ASN ** R 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 152 ASN D 168 GLN E 122 ASN ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** 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 c 45 HIS 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: 0.7213 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.937 102738 Z= 0.424 Angle : 0.727 33.609 154088 Z= 0.377 Chirality : 0.040 0.922 19729 Planarity : 0.006 0.086 7951 Dihedral : 24.379 179.527 52293 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.34 % Favored : 94.43 % Rotamer: Outliers : 4.33 % Allowed : 18.09 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 1.24 % Twisted Proline : 0.72 % 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: -1.42 (0.13), residues: 3485 helix: -0.51 (0.15), residues: 1002 sheet: -0.22 (0.21), residues: 559 loop : -1.40 (0.13), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP Q 61 HIS 0.012 0.002 HIS J 41 PHE 0.036 0.002 PHE R 3 TYR 0.076 0.003 TYR R 431 ARG 0.011 0.001 ARG R 296 *********************** 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 1150 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1022 time to evaluate : 3.918 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: C 247 MET cc_start: 0.6280 (mmm) cc_final: 0.6041 (mmm) REVERT: G 72 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7088 (tt) REVERT: J 97 TYR cc_start: 0.7035 (OUTLIER) cc_final: 0.6402 (p90) REVERT: b 54 ILE cc_start: 0.6800 (tp) cc_final: 0.6587 (tp) REVERT: i 27 ASN cc_start: 0.5970 (t0) cc_final: 0.5514 (t0) outliers start: 128 outliers final: 80 residues processed: 1074 average time/residue: 0.9200 time to fit residues: 1667.1801 Evaluate side-chains 1014 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 932 time to evaluate : 3.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 263 GLU Chi-restraints excluded: chain R residue 285 ASP Chi-restraints excluded: chain R residue 351 TYR Chi-restraints excluded: chain R residue 353 ASP Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain F residue 112 ARG Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain L residue 119 LYS Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain S residue 6 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain V residue 86 LYS Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 25 SER Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 19 THR Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain h residue 3 ASP Chi-restraints excluded: chain h residue 12 VAL Chi-restraints excluded: chain h residue 31 ASP Chi-restraints excluded: chain h residue 35 ASN Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain i residue 25 LEU Chi-restraints excluded: chain i residue 44 ARG Chi-restraints excluded: chain i residue 50 ILE 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: 0.7980 chunk 162 optimal weight: 10.0000 chunk 590 optimal weight: 4.9990 chunk 637 optimal weight: 1.9990 chunk 525 optimal weight: 3.9990 chunk 585 optimal weight: 4.9990 chunk 201 optimal weight: 20.0000 chunk 473 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 300 ASN ** R 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 350 ASN ** R 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 37 GLN ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 GLN ** D 191 ASN ** 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 59 GLN N 27 ASN ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 HIS Q 91 ASN ** U 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 48 GLN d 26 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.968 102738 Z= 0.359 Angle : 0.631 33.569 154088 Z= 0.328 Chirality : 0.036 0.456 19729 Planarity : 0.005 0.093 7951 Dihedral : 24.364 179.971 52282 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.34 % Favored : 94.55 % Rotamer: Outliers : 4.19 % Allowed : 21.61 % Favored : 74.20 % 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: -1.12 (0.13), residues: 3485 helix: -0.00 (0.16), residues: 990 sheet: -0.25 (0.21), residues: 578 loop : -1.30 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP Q 61 HIS 0.018 0.002 HIS R 259 PHE 0.028 0.002 PHE F 99 TYR 0.039 0.002 TYR R 351 ARG 0.009 0.001 ARG i 47 *********************** 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 1125 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1001 time to evaluate : 3.908 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: R 20 MET cc_start: 0.2220 (tpp) cc_final: 0.1961 (tpt) REVERT: R 123 MET cc_start: -0.0477 (mtt) cc_final: -0.0888 (ttm) REVERT: C 247 MET cc_start: 0.6260 (mmm) cc_final: 0.5834 (mmm) REVERT: J 97 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.6668 (p90) REVERT: K 44 LYS cc_start: 0.7954 (mmtt) cc_final: 0.7647 (mmtt) REVERT: M 27 VAL cc_start: 0.7718 (p) cc_final: 0.7452 (p) REVERT: M 116 GLU cc_start: 0.3969 (tp30) cc_final: 0.3624 (tp30) REVERT: N 92 GLU cc_start: 0.5642 (pm20) cc_final: 0.5001 (pm20) REVERT: Z 20 ARG cc_start: 0.6968 (mtm110) cc_final: 0.6646 (mtm110) REVERT: h 74 SER cc_start: 0.8279 (t) cc_final: 0.7749 (m) outliers start: 124 outliers final: 85 residues processed: 1047 average time/residue: 0.9084 time to fit residues: 1609.6596 Evaluate side-chains 1018 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 932 time to evaluate : 3.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 351 TYR Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain F residue 3 ARG Chi-restraints excluded: chain F residue 112 ARG Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 84 CYS Chi-restraints excluded: chain K residue 92 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 103 LYS Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 98 LEU Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain S residue 6 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 63 ILE Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain V residue 19 LYS Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 25 SER Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain h residue 31 ASP Chi-restraints excluded: chain h residue 35 ASN Chi-restraints excluded: chain h residue 50 LYS Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain i residue 44 ARG Chi-restraints excluded: chain i residue 55 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 583 optimal weight: 7.9990 chunk 443 optimal weight: 5.9990 chunk 306 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 281 optimal weight: 7.9990 chunk 396 optimal weight: 10.0000 chunk 592 optimal weight: 10.0000 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: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 103 HIS R 307 ASN ** R 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 HIS ** 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 48 HIS J 59 ASN J 118 GLN J 131 HIS K 3 GLN L 59 GLN ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 103 HIS Q 91 ASN ** U 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 19 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.958 102738 Z= 0.633 Angle : 0.852 33.334 154088 Z= 0.433 Chirality : 0.046 0.377 19729 Planarity : 0.006 0.082 7951 Dihedral : 24.536 179.564 52279 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.23 % Favored : 93.63 % Rotamer: Outliers : 6.66 % Allowed : 23.54 % Favored : 69.80 % 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: -1.37 (0.13), residues: 3485 helix: -0.09 (0.16), residues: 975 sheet: -0.47 (0.21), residues: 564 loop : -1.49 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Q 61 HIS 0.021 0.002 HIS O 103 PHE 0.055 0.003 PHE D 79 TYR 0.037 0.003 TYR R 351 ARG 0.025 0.001 ARG G 36 *********************** 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 1144 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 947 time to evaluate : 4.063 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: R 6 MET cc_start: 0.1741 (ptp) cc_final: 0.1131 (mmm) REVERT: R 123 MET cc_start: -0.0974 (mtt) cc_final: -0.2545 (ttm) REVERT: R 338 MET cc_start: -0.0391 (mmm) cc_final: -0.0602 (ttt) REVERT: C 244 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7875 (ptpt) REVERT: D 140 HIS cc_start: 0.7997 (OUTLIER) cc_final: 0.7420 (p90) REVERT: J 97 TYR cc_start: 0.7368 (OUTLIER) cc_final: 0.6685 (p90) REVERT: J 106 ILE cc_start: 0.8388 (mm) cc_final: 0.8132 (mm) REVERT: K 44 LYS cc_start: 0.7947 (mmtt) cc_final: 0.7708 (mmtt) REVERT: L 1 MET cc_start: 0.6099 (tpt) cc_final: 0.5629 (tpt) REVERT: M 28 HIS cc_start: 0.7028 (p-80) cc_final: 0.6779 (p90) REVERT: Q 76 TYR cc_start: 0.8068 (t80) cc_final: 0.7757 (t80) REVERT: S 69 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.6927 (mm) REVERT: V 32 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7902 (mmtm) REVERT: X 52 ARG cc_start: 0.7461 (tpt170) cc_final: 0.7096 (tpt170) REVERT: f 20 LYS cc_start: 0.7939 (mmmt) cc_final: 0.7676 (tptp) REVERT: h 72 MET cc_start: 0.7048 (tpp) cc_final: 0.6785 (tpp) REVERT: i 27 ASN cc_start: 0.6330 (t0) cc_final: 0.5838 (t0) REVERT: i 28 LEU cc_start: 0.6655 (mp) cc_final: 0.6440 (mp) outliers start: 197 outliers final: 132 residues processed: 1027 average time/residue: 0.9087 time to fit residues: 1580.9161 Evaluate side-chains 1030 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 894 time to evaluate : 3.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 351 TYR Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain R residue 368 THR Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 3 ARG Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 112 ARG Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 84 CYS Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain S residue 6 VAL Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 63 ILE Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain V residue 19 LYS Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 31 VAL Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain c residue 10 THR Chi-restraints excluded: chain c residue 14 GLU Chi-restraints excluded: chain c residue 18 ILE Chi-restraints excluded: chain c residue 43 THR Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 65 ILE Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 28 GLU Chi-restraints excluded: chain g residue 12 ILE Chi-restraints excluded: chain g residue 19 THR Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain g residue 101 ASN Chi-restraints excluded: chain h residue 31 ASP Chi-restraints excluded: chain h residue 35 ASN Chi-restraints excluded: chain h residue 37 THR Chi-restraints excluded: chain h residue 45 SER Chi-restraints excluded: chain h residue 50 LYS Chi-restraints excluded: chain h residue 56 ILE Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 30 PHE Chi-restraints excluded: chain i residue 55 THR 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: 6.9990 chunk 9 optimal weight: 30.0000 chunk 467 optimal weight: 1.9990 chunk 258 optimal weight: 50.0000 chunk 535 optimal weight: 2.9990 chunk 433 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 320 optimal weight: 10.0000 chunk 563 optimal weight: 6.9990 chunk 158 optimal weight: 30.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN D 173 ASN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** 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 L 59 GLN ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 91 ASN ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 67 ASN Z 19 GLN a 15 GLN ** g 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.959 102738 Z= 0.403 Angle : 0.680 33.439 154088 Z= 0.350 Chirality : 0.038 0.322 19729 Planarity : 0.005 0.133 7951 Dihedral : 24.543 179.325 52279 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.85 % Favored : 94.03 % Rotamer: Outliers : 5.48 % Allowed : 25.70 % Favored : 68.82 % 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: 0.14 (0.16), residues: 977 sheet: -0.39 (0.21), residues: 574 loop : -1.41 (0.13), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 250 HIS 0.020 0.001 HIS O 103 PHE 0.031 0.002 PHE Q 106 TYR 0.037 0.002 TYR R 351 ARG 0.009 0.001 ARG F 115 *********************** 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 1106 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 944 time to evaluate : 3.966 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: R 6 MET cc_start: 0.1656 (ptp) cc_final: 0.1204 (mmm) REVERT: R 123 MET cc_start: -0.0603 (mtt) cc_final: -0.1281 (ttm) REVERT: D 140 HIS cc_start: 0.7742 (OUTLIER) cc_final: 0.7242 (p90) REVERT: D 183 ARG cc_start: 0.6431 (OUTLIER) cc_final: 0.6019 (ttm-80) REVERT: E 82 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7202 (pm20) REVERT: F 168 GLU cc_start: 0.3903 (pt0) cc_final: 0.3656 (pt0) REVERT: J 97 TYR cc_start: 0.7376 (OUTLIER) cc_final: 0.6898 (p90) REVERT: J 106 ILE cc_start: 0.8209 (mm) cc_final: 0.7970 (mm) REVERT: L 1 MET cc_start: 0.6054 (tpt) cc_final: 0.5678 (tpt) REVERT: L 16 ARG cc_start: 0.7899 (ttm170) cc_final: 0.7612 (ttm170) REVERT: N 82 LYS cc_start: 0.7613 (ttpt) cc_final: 0.7379 (ttpt) REVERT: U 40 MET cc_start: 0.5508 (mmm) cc_final: 0.4849 (mmm) REVERT: f 20 LYS cc_start: 0.7908 (mmmt) cc_final: 0.7693 (tptp) REVERT: h 5 ARG cc_start: 0.7575 (mmm-85) cc_final: 0.7320 (mtt90) REVERT: i 25 LEU cc_start: 0.7303 (tt) cc_final: 0.7012 (tt) REVERT: i 27 ASN cc_start: 0.6121 (t0) cc_final: 0.5474 (t0) outliers start: 162 outliers final: 112 residues processed: 1013 average time/residue: 0.9298 time to fit residues: 1599.9330 Evaluate side-chains 997 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 881 time to evaluate : 3.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 351 TYR Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain R residue 368 THR Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain F residue 3 ARG Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 84 CYS Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 69 ILE Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain S residue 6 VAL Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain U residue 58 ASN Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 25 SER Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain a residue 20 LEU Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 31 VAL Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 60 GLU Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain a residue 116 ILE Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain c residue 10 THR Chi-restraints excluded: chain c residue 14 GLU Chi-restraints excluded: chain c residue 43 THR Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 28 GLU Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain h residue 31 ASP Chi-restraints excluded: chain h residue 35 ASN Chi-restraints excluded: chain h residue 50 LYS Chi-restraints excluded: chain h residue 56 ILE Chi-restraints excluded: chain h residue 73 THR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 30 PHE Chi-restraints excluded: chain i residue 55 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 211 optimal weight: 8.9990 chunk 564 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 368 optimal weight: 0.0970 chunk 154 optimal weight: 50.0000 chunk 627 optimal weight: 9.9990 chunk 521 optimal weight: 3.9990 chunk 290 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 329 optimal weight: 10.0000 overall best weight: 5.6186 ------------------------------------------------------------------------------- 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 R 372 ASN C 153 GLN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 ASN F 178 GLN ** J 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** 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 ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 ASN Z 19 GLN a 15 GLN c 4 ASN ** g 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 39 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.961 102738 Z= 0.495 Angle : 0.735 33.328 154088 Z= 0.376 Chirality : 0.041 0.389 19729 Planarity : 0.005 0.075 7951 Dihedral : 24.530 179.984 52279 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.80 % Favored : 93.11 % Rotamer: Outliers : 6.39 % Allowed : 26.99 % Favored : 66.62 % 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: -1.29 (0.13), residues: 3485 helix: 0.14 (0.16), residues: 979 sheet: -0.62 (0.21), residues: 560 loop : -1.47 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP M 65 HIS 0.019 0.002 HIS O 103 PHE 0.030 0.002 PHE D 79 TYR 0.048 0.002 TYR M 9 ARG 0.011 0.001 ARG O 105 *********************** 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 1093 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 904 time to evaluate : 4.018 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: R 6 MET cc_start: 0.1788 (ptp) cc_final: 0.1315 (mmm) REVERT: R 432 LEU cc_start: -0.3109 (OUTLIER) cc_final: -0.3518 (pp) REVERT: D 140 HIS cc_start: 0.7886 (OUTLIER) cc_final: 0.7365 (p90) REVERT: D 183 ARG cc_start: 0.6703 (OUTLIER) cc_final: 0.6181 (ttm-80) REVERT: E 82 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7307 (pm20) REVERT: J 97 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.6874 (p90) REVERT: J 106 ILE cc_start: 0.8311 (mm) cc_final: 0.8105 (mm) REVERT: L 1 MET cc_start: 0.6332 (tpt) cc_final: 0.5926 (tpt) REVERT: L 16 ARG cc_start: 0.7966 (ttm170) cc_final: 0.7688 (ttm170) REVERT: L 71 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6981 (ttt-90) REVERT: g 2 TYR cc_start: 0.6225 (p90) cc_final: 0.5951 (p90) REVERT: h 69 TYR cc_start: 0.6830 (m-10) cc_final: 0.6169 (m-10) REVERT: i 48 LYS cc_start: 0.6985 (mmtm) cc_final: 0.6610 (mmmt) outliers start: 189 outliers final: 145 residues processed: 981 average time/residue: 0.9931 time to fit residues: 1659.9229 Evaluate side-chains 1028 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 877 time to evaluate : 3.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 351 TYR Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain R residue 368 THR Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain F residue 3 ARG Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain I residue 30 GLN Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 84 CYS Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 69 ILE Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 94 MET Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain S residue 6 VAL Chi-restraints excluded: chain S residue 9 THR Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 34 SER Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 68 ASN Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain V residue 19 LYS Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain X residue 5 CYS Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 25 SER Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain Z residue 43 ILE Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 20 LEU Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 31 VAL Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 60 GLU Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain a residue 116 ILE Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 24 VAL Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 52 LYS Chi-restraints excluded: chain c residue 10 THR Chi-restraints excluded: chain c residue 14 GLU Chi-restraints excluded: chain c residue 43 THR Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 25 SER Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 65 ILE Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 28 GLU Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain g residue 101 ASN Chi-restraints excluded: chain h residue 35 ASN Chi-restraints excluded: chain h residue 37 THR Chi-restraints excluded: chain h residue 45 SER Chi-restraints excluded: chain h residue 50 LYS Chi-restraints excluded: chain h residue 56 ILE Chi-restraints excluded: chain h residue 70 THR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain i residue 4 ASN Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 30 PHE Chi-restraints excluded: chain i residue 39 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 605 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 357 optimal weight: 9.9990 chunk 458 optimal weight: 50.0000 chunk 355 optimal weight: 6.9990 chunk 528 optimal weight: 30.0000 chunk 350 optimal weight: 3.9990 chunk 625 optimal weight: 8.9990 chunk 391 optimal weight: 0.8980 chunk 381 optimal weight: 6.9990 chunk 288 optimal weight: 5.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 ASN L 54 GLN 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 Z 19 GLN a 15 GLN c 4 ASN ** g 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 39 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.962 102738 Z= 0.455 Angle : 0.711 33.251 154088 Z= 0.365 Chirality : 0.040 0.345 19729 Planarity : 0.005 0.072 7951 Dihedral : 24.552 179.751 52279 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.63 % Favored : 93.29 % Rotamer: Outliers : 5.75 % Allowed : 28.64 % Favored : 65.61 % 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: 0.14 (0.16), residues: 976 sheet: -0.62 (0.21), residues: 576 loop : -1.50 (0.13), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP M 65 HIS 0.009 0.001 HIS J 41 PHE 0.032 0.002 PHE J 120 TYR 0.035 0.002 TYR R 351 ARG 0.020 0.001 ARG G 36 *********************** 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 1068 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 898 time to evaluate : 3.996 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: R 6 MET cc_start: 0.1752 (ptp) cc_final: 0.1316 (mmm) REVERT: R 432 LEU cc_start: -0.2899 (OUTLIER) cc_final: -0.3455 (pp) REVERT: D 140 HIS cc_start: 0.7809 (OUTLIER) cc_final: 0.7288 (p90) REVERT: D 183 ARG cc_start: 0.6742 (OUTLIER) cc_final: 0.6105 (ttm-80) REVERT: J 97 TYR cc_start: 0.7396 (OUTLIER) cc_final: 0.6855 (p90) REVERT: J 106 ILE cc_start: 0.8277 (mm) cc_final: 0.8020 (mm) REVERT: L 1 MET cc_start: 0.6238 (tpt) cc_final: 0.5843 (tpt) REVERT: i 48 LYS cc_start: 0.6950 (mmtm) cc_final: 0.6653 (mmmt) outliers start: 170 outliers final: 142 residues processed: 972 average time/residue: 0.9073 time to fit residues: 1498.8516 Evaluate side-chains 1005 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 859 time to evaluate : 3.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 351 TYR Chi-restraints excluded: chain R residue 368 THR Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain I residue 30 GLN Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 84 CYS Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 69 ILE Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 94 MET Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain S residue 2 GLN Chi-restraints excluded: chain S residue 6 VAL Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 34 SER Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 68 ASN Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain V residue 19 LYS Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain X residue 5 CYS Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 25 SER Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 20 LEU Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 31 VAL Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain a residue 116 ILE Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 24 VAL Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 52 LYS Chi-restraints excluded: chain c residue 10 THR Chi-restraints excluded: chain c residue 14 GLU Chi-restraints excluded: chain c residue 42 SER Chi-restraints excluded: chain c residue 43 THR Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 25 SER Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 64 ASN Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 28 GLU Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain g residue 101 ASN Chi-restraints excluded: chain h residue 45 SER Chi-restraints excluded: chain h residue 50 LYS Chi-restraints excluded: chain h residue 56 ILE Chi-restraints excluded: chain h residue 70 THR Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain i residue 4 ASN Chi-restraints excluded: chain i residue 5 GLU Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 30 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 386 optimal weight: 0.0980 chunk 249 optimal weight: 6.9990 chunk 373 optimal weight: 5.9990 chunk 188 optimal weight: 20.0000 chunk 122 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 397 optimal weight: 0.9980 chunk 426 optimal weight: 7.9990 chunk 309 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 491 optimal weight: 0.8980 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 191 ASN ** 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 188 ASN ** 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 L 4 HIS L 59 GLN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 91 ASN ** Q 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 2 GLN S 68 ASN Z 19 GLN ** 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: 0.7348 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.965 102738 Z= 0.368 Angle : 0.664 33.206 154088 Z= 0.342 Chirality : 0.037 0.315 19729 Planarity : 0.005 0.071 7951 Dihedral : 24.539 179.852 52277 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.80 % Favored : 93.11 % Rotamer: Outliers : 4.90 % Allowed : 29.83 % Favored : 65.27 % 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: -1.25 (0.13), residues: 3485 helix: 0.20 (0.16), residues: 979 sheet: -0.68 (0.21), residues: 604 loop : -1.44 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 250 HIS 0.013 0.001 HIS G 66 PHE 0.029 0.002 PHE D 79 TYR 0.035 0.002 TYR J 76 ARG 0.012 0.001 ARG G 36 *********************** 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 1037 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 892 time to evaluate : 4.054 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: R 6 MET cc_start: 0.1737 (ptp) cc_final: 0.1311 (mmm) REVERT: R 347 GLU cc_start: 0.2364 (mm-30) cc_final: 0.1876 (mm-30) REVERT: R 432 LEU cc_start: -0.2821 (OUTLIER) cc_final: -0.3424 (pp) REVERT: D 140 HIS cc_start: 0.7726 (OUTLIER) cc_final: 0.7189 (p90) REVERT: D 183 ARG cc_start: 0.6707 (OUTLIER) cc_final: 0.6104 (ttm-80) REVERT: E 82 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7266 (pm20) REVERT: E 188 ASN cc_start: 0.6096 (OUTLIER) cc_final: 0.5422 (t0) REVERT: J 97 TYR cc_start: 0.7333 (OUTLIER) cc_final: 0.6840 (p90) REVERT: J 106 ILE cc_start: 0.8198 (mm) cc_final: 0.7967 (mm) REVERT: L 1 MET cc_start: 0.6114 (tpt) cc_final: 0.5799 (tpt) REVERT: N 12 GLN cc_start: 0.6770 (OUTLIER) cc_final: 0.6512 (mt0) REVERT: i 48 LYS cc_start: 0.6833 (mmtm) cc_final: 0.6581 (mmmt) outliers start: 145 outliers final: 120 residues processed: 960 average time/residue: 1.0217 time to fit residues: 1689.8057 Evaluate side-chains 988 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 861 time to evaluate : 3.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 351 TYR Chi-restraints excluded: chain R residue 368 THR Chi-restraints excluded: chain R residue 390 VAL Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain I residue 30 GLN Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 59 LYS Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 84 CYS Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 69 ILE Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 94 MET Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain S residue 6 VAL Chi-restraints excluded: chain S residue 9 THR Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 34 SER Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 68 ASN Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain V residue 19 LYS Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 25 SER Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 20 LEU Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 31 VAL Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 116 ILE Chi-restraints excluded: chain b residue 24 VAL Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 52 LYS Chi-restraints excluded: chain c residue 14 GLU Chi-restraints excluded: chain c residue 42 SER Chi-restraints excluded: chain c residue 43 THR Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 65 ILE Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 28 GLU Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain h residue 50 LYS Chi-restraints excluded: chain h residue 56 ILE Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 83 LEU Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain i residue 4 ASN Chi-restraints excluded: chain i residue 43 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 569 optimal weight: 8.9990 chunk 599 optimal weight: 20.0000 chunk 546 optimal weight: 9.9990 chunk 582 optimal weight: 4.9990 chunk 350 optimal weight: 1.9990 chunk 253 optimal weight: 7.9990 chunk 457 optimal weight: 30.0000 chunk 178 optimal weight: 8.9990 chunk 526 optimal weight: 9.9990 chunk 551 optimal weight: 1.9990 chunk 580 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 191 ASN ** 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 122 ASN E 188 ASN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 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** O 49 ASN ** O 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 91 ASN ** Q 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 ASN Z 19 GLN c 4 ASN ** g 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.964 102738 Z= 0.395 Angle : 0.678 33.186 154088 Z= 0.349 Chirality : 0.037 0.325 19729 Planarity : 0.005 0.069 7951 Dihedral : 24.502 179.894 52277 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.94 % Favored : 92.97 % Rotamer: Outliers : 5.14 % Allowed : 29.49 % Favored : 65.37 % 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: -1.29 (0.13), residues: 3485 helix: 0.11 (0.16), residues: 988 sheet: -0.67 (0.21), residues: 607 loop : -1.46 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 250 HIS 0.013 0.001 HIS G 66 PHE 0.030 0.002 PHE D 79 TYR 0.034 0.002 TYR R 351 ARG 0.012 0.001 ARG G 36 *********************** 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 1032 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 880 time to evaluate : 4.192 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: R 432 LEU cc_start: -0.2893 (OUTLIER) cc_final: -0.3621 (pp) REVERT: D 46 TYR cc_start: 0.7237 (p90) cc_final: 0.7012 (p90) REVERT: D 140 HIS cc_start: 0.7736 (OUTLIER) cc_final: 0.7272 (p90) REVERT: D 183 ARG cc_start: 0.6751 (OUTLIER) cc_final: 0.6134 (ttm-80) REVERT: E 82 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7319 (pm20) REVERT: J 97 TYR cc_start: 0.7397 (OUTLIER) cc_final: 0.6852 (p90) REVERT: J 106 ILE cc_start: 0.8261 (mm) cc_final: 0.8027 (mm) REVERT: L 1 MET cc_start: 0.6142 (tpt) cc_final: 0.5854 (tpt) REVERT: N 12 GLN cc_start: 0.6803 (OUTLIER) cc_final: 0.6530 (mt0) outliers start: 152 outliers final: 128 residues processed: 956 average time/residue: 0.9398 time to fit residues: 1529.9322 Evaluate side-chains 988 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 854 time to evaluate : 3.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 351 TYR Chi-restraints excluded: chain R residue 368 THR Chi-restraints excluded: chain R residue 390 VAL Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain I residue 30 GLN Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 84 CYS Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 69 ILE Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 94 MET Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain S residue 6 VAL Chi-restraints excluded: chain S residue 9 THR Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 34 SER Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 68 ASN Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain V residue 19 LYS Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain X residue 5 CYS Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 20 LEU Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 116 ILE Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 52 LYS Chi-restraints excluded: chain c residue 14 GLU Chi-restraints excluded: chain c residue 42 SER Chi-restraints excluded: chain c residue 43 THR Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 25 SER Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 65 ILE Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 28 GLU Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain g residue 101 ASN Chi-restraints excluded: chain h residue 50 LYS Chi-restraints excluded: chain h residue 56 ILE Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 83 LEU Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain i residue 4 ASN Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 43 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 382 optimal weight: 0.0670 chunk 616 optimal weight: 2.9990 chunk 376 optimal weight: 0.9980 chunk 292 optimal weight: 10.0000 chunk 428 optimal weight: 40.0000 chunk 646 optimal weight: 1.9990 chunk 595 optimal weight: 7.9990 chunk 514 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 397 optimal weight: 4.9990 chunk 315 optimal weight: 10.0000 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 300 ASN ** D 191 ASN ** 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 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 HIS ** 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** ** O 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 91 ASN S 68 ASN Z 19 GLN c 4 ASN ** g 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.4699 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= 0.322 Angle : 0.636 33.169 154088 Z= 0.327 Chirality : 0.034 0.288 19729 Planarity : 0.004 0.070 7951 Dihedral : 24.476 179.834 52277 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.60 % Favored : 93.31 % Rotamer: Outliers : 3.38 % Allowed : 31.59 % Favored : 65.03 % 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: -1.19 (0.14), residues: 3485 helix: 0.09 (0.16), residues: 986 sheet: -0.49 (0.21), residues: 598 loop : -1.37 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 65 HIS 0.013 0.001 HIS G 66 PHE 0.023 0.002 PHE i 30 TYR 0.034 0.002 TYR R 351 ARG 0.030 0.001 ARG G 36 ********************** 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 986 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 886 time to evaluate : 3.985 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: R 432 LEU cc_start: -0.3292 (OUTLIER) cc_final: -0.3858 (pp) REVERT: D 168 GLN cc_start: 0.7661 (tt0) cc_final: 0.7254 (tt0) REVERT: D 183 ARG cc_start: 0.6554 (OUTLIER) cc_final: 0.5854 (ttm-80) REVERT: E 82 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7270 (pm20) REVERT: G 72 LEU cc_start: 0.6271 (tt) cc_final: 0.6005 (tp) REVERT: J 97 TYR cc_start: 0.7256 (OUTLIER) cc_final: 0.6597 (p90) REVERT: J 106 ILE cc_start: 0.8148 (mm) cc_final: 0.7884 (mm) REVERT: L 1 MET cc_start: 0.5903 (tpt) cc_final: 0.5608 (tpt) REVERT: M 1 MET cc_start: 0.6018 (OUTLIER) cc_final: 0.5750 (mmm) REVERT: Q 76 TYR cc_start: 0.7802 (t80) cc_final: 0.7587 (t80) REVERT: U 92 ARG cc_start: 0.7551 (mtm-85) cc_final: 0.7339 (mtm110) REVERT: V 32 LYS cc_start: 0.7780 (mmtt) cc_final: 0.7505 (mmtm) REVERT: V 54 TYR cc_start: 0.7394 (m-80) cc_final: 0.7138 (m-80) REVERT: e 32 LEU cc_start: 0.7869 (mt) cc_final: 0.7545 (mt) REVERT: h 74 SER cc_start: 0.8463 (t) cc_final: 0.7886 (m) outliers start: 100 outliers final: 84 residues processed: 938 average time/residue: 0.8988 time to fit residues: 1437.2568 Evaluate side-chains 951 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 862 time to evaluate : 3.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 368 THR Chi-restraints excluded: chain R residue 390 VAL Chi-restraints excluded: chain R residue 432 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain I residue 30 GLN Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 84 CYS Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 69 ILE Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 94 MET Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain S residue 6 VAL Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 34 SER Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 68 ASN Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain V residue 19 LYS Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain X residue 5 CYS Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 20 LEU Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 116 ILE Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 52 LYS Chi-restraints excluded: chain c residue 42 SER Chi-restraints excluded: chain c residue 43 THR Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 28 GLU Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain h residue 81 VAL Chi-restraints excluded: chain h residue 83 LEU Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain i residue 4 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 408 optimal weight: 0.7980 chunk 548 optimal weight: 0.9990 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: 9.9990 chunk 215 optimal weight: 10.0000 chunk 529 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- 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** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 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** ** O 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN S 68 ASN ** U 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 19 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.104360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.065701 restraints weight = 249483.361| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.72 r_work: 0.2805 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.976 102738 Z= 0.491 Angle : 0.737 32.669 154088 Z= 0.377 Chirality : 0.041 0.357 19729 Planarity : 0.005 0.068 7951 Dihedral : 24.462 179.890 52277 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.37 % Favored : 92.54 % Rotamer: Outliers : 4.06 % Allowed : 30.44 % Favored : 65.51 % 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: -1.30 (0.13), residues: 3485 helix: 0.01 (0.16), residues: 985 sheet: -0.63 (0.21), residues: 591 loop : -1.42 (0.13), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP M 65 HIS 0.013 0.002 HIS E 189 PHE 0.038 0.002 PHE J 120 TYR 0.023 0.002 TYR c 35 ARG 0.022 0.001 ARG R 395 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26604.90 seconds wall clock time: 466 minutes 44.30 seconds (28004.30 seconds total)