Starting phenix.real_space_refine on Thu Feb 22 00:02:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zet_6922/02_2024/5zet_6922.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zet_6922/02_2024/5zet_6922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zet_6922/02_2024/5zet_6922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zet_6922/02_2024/5zet_6922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zet_6922/02_2024/5zet_6922.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zet_6922/02_2024/5zet_6922.pdb" } resolution = 3.2 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= 0.002 sd= 0.027 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 3219 5.49 5 S 60 5.16 5 C 48383 2.51 5 N 18204 2.21 5 O 27508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 23": "OE1" <-> "OE2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C ARG 258": "NH1" <-> "NH2" Residue "D PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 46": "NH1" <-> "NH2" Residue "E ARG 55": "NH1" <-> "NH2" Residue "E TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 75": "NH1" <-> "NH2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E ARG 118": "NH1" <-> "NH2" Residue "E ARG 120": "NH1" <-> "NH2" Residue "E ARG 160": "NH1" <-> "NH2" Residue "F ARG 14": "NH1" <-> "NH2" Residue "F ARG 16": "NH1" <-> "NH2" Residue "F ASP 49": "OD1" <-> "OD2" Residue "F ARG 52": "NH1" <-> "NH2" Residue "F ARG 78": "NH1" <-> "NH2" Residue "F ARG 99": "NH1" <-> "NH2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "F ASP 108": "OD1" <-> "OD2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 155": "NH1" <-> "NH2" Residue "F ARG 178": "NH1" <-> "NH2" Residue "F PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 99": "NH1" <-> "NH2" Residue "K PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 7": "NH1" <-> "NH2" Residue "L ARG 30": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L ARG 69": "NH1" <-> "NH2" Residue "L ARG 70": "NH1" <-> "NH2" Residue "L ARG 71": "NH1" <-> "NH2" Residue "L PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 92": "OD1" <-> "OD2" Residue "L ARG 94": "NH1" <-> "NH2" Residue "L ARG 104": "NH1" <-> "NH2" Residue "L ARG 107": "NH1" <-> "NH2" Residue "M PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 18": "NH1" <-> "NH2" Residue "N TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "N ARG 51": "NH1" <-> "NH2" Residue "N ARG 56": "NH1" <-> "NH2" Residue "N ARG 60": "NH1" <-> "NH2" Residue "N ARG 101": "NH1" <-> "NH2" Residue "N ARG 120": "NH1" <-> "NH2" Residue "N ARG 134": "NH1" <-> "NH2" Residue "O ARG 33": "NH1" <-> "NH2" Residue "O ARG 42": "NH1" <-> "NH2" Residue "O ARG 45": "NH1" <-> "NH2" Residue "O TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 63": "NH1" <-> "NH2" Residue "O PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 90": "NH1" <-> "NH2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "R ARG 3": "NH1" <-> "NH2" Residue "T GLU 6": "OE1" <-> "OE2" Residue "T ARG 18": "NH1" <-> "NH2" Residue "T ARG 25": "NH1" <-> "NH2" Residue "T ARG 32": "NH1" <-> "NH2" Residue "T ARG 44": "NH1" <-> "NH2" Residue "T ASP 84": "OD1" <-> "OD2" Residue "T ARG 91": "NH1" <-> "NH2" Residue "T ARG 106": "NH1" <-> "NH2" Residue "U ASP 6": "OD1" <-> "OD2" Residue "U ARG 66": "NH1" <-> "NH2" Residue "U ARG 70": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 30": "NH1" <-> "NH2" Residue "V ARG 40": "NH1" <-> "NH2" Residue "V ARG 82": "NH1" <-> "NH2" Residue "V TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 86": "NH1" <-> "NH2" Residue "V ARG 96": "NH1" <-> "NH2" Residue "W ARG 16": "NH1" <-> "NH2" Residue "W ARG 28": "NH1" <-> "NH2" Residue "W ARG 29": "NH1" <-> "NH2" Residue "W TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 52": "NH1" <-> "NH2" Residue "W ARG 59": "NH1" <-> "NH2" Residue "W ARG 89": "NH1" <-> "NH2" Residue "W ARG 90": "NH1" <-> "NH2" Residue "X ARG 14": "NH1" <-> "NH2" Residue "X ARG 20": "NH1" <-> "NH2" Residue "X ARG 25": "NH1" <-> "NH2" Residue "X ARG 39": "NH1" <-> "NH2" Residue "X ARG 41": "NH1" <-> "NH2" Residue "X ARG 53": "NH1" <-> "NH2" Residue "X ARG 75": "NH1" <-> "NH2" Residue "X ARG 85": "NH1" <-> "NH2" Residue "Z ARG 11": "NH1" <-> "NH2" Residue "Z ARG 23": "NH1" <-> "NH2" Residue "Z ARG 33": "NH1" <-> "NH2" Residue "Z ARG 45": "NH1" <-> "NH2" Residue "Z ARG 46": "NH1" <-> "NH2" Residue "Z ARG 62": "NH1" <-> "NH2" Residue "Z GLU 65": "OE1" <-> "OE2" Residue "1 ARG 16": "NH1" <-> "NH2" Residue "1 ARG 20": "NH1" <-> "NH2" Residue "1 ARG 37": "NH1" <-> "NH2" Residue "1 ARG 44": "NH1" <-> "NH2" Residue "2 TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 62": "OE1" <-> "OE2" Residue "4 ARG 8": "NH1" <-> "NH2" Residue "4 ARG 21": "NH1" <-> "NH2" Residue "4 ARG 29": "NH1" <-> "NH2" Residue "4 ARG 30": "NH1" <-> "NH2" Residue "4 ASP 34": "OD1" <-> "OD2" Residue "4 ARG 35": "NH1" <-> "NH2" Residue "5 ARG 15": "NH1" <-> "NH2" Residue "5 ARG 24": "NH1" <-> "NH2" Residue "5 ARG 37": "NH1" <-> "NH2" Residue "5 ARG 43": "NH1" <-> "NH2" Residue "6 ARG 13": "NH1" <-> "NH2" Residue "6 ARG 15": "NH1" <-> "NH2" Residue "6 ARG 16": "NH1" <-> "NH2" Residue "6 ARG 24": "NH1" <-> "NH2" Residue "6 ARG 40": "NH1" <-> "NH2" Residue "6 ARG 42": "NH1" <-> "NH2" Residue "6 ARG 43": "NH1" <-> "NH2" Residue "6 ARG 47": "NH1" <-> "NH2" Residue "6 ARG 57": "NH1" <-> "NH2" Residue "7 ARG 15": "NH1" <-> "NH2" Residue "7 ARG 18": "NH1" <-> "NH2" Residue "7 ARG 22": "NH1" <-> "NH2" Residue "7 ARG 31": "NH1" <-> "NH2" Residue "7 ARG 35": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 97374 Number of models: 1 Model: "" Number of chains: 34 Chain: "C" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2097 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 19, 'TRANS': 253} Chain: "D" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1587 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain: "E" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1553 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 11, 'TRANS': 195} Chain: "F" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1437 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 8, 'TRANS': 172} Chain: "G" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1348 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "H" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1018 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 3, 'TRANS': 147} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 68 Chain: "I" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 918 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain: "J" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 990 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 8, 'TRANS': 124} Chain: "K" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1138 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 11, 'TRANS': 135} Chain: "L" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 930 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "M" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "N" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1074 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "O" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 919 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "P" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 956 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "Q" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 907 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "R" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "S" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 768 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "T" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 873 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 8, 'TRANS': 105} Chain: "U" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 739 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "V" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 731 Classifications: {'peptide': 97} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 92} Chain: "W" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1407 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 9, 'TRANS': 178} Chain: "X" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 604 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "Y" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 470 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "Z" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 527 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "B" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2501 Classifications: {'RNA': 117} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 60, 'rna3p_pyr': 51} Link IDs: {'rna2p': 6, 'rna3p': 110} Chain: "A" Number of atoms: 66623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3102, 66623 Classifications: {'RNA': 3102} Modifications used: {'rna2p_pur': 297, 'rna2p_pyr': 147, 'rna3p_pur': 1479, 'rna3p_pyr': 1179} Link IDs: {'rna2p': 444, 'rna3p': 2657} Chain breaks: 5 Chain: "1" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 483 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "2" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 510 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "3" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "4" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 416 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 4, 'TRANS': 45} Chain: "5" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 372 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "6" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 502 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "7" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 298 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "8" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 189 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Time building chain proxies: 36.57, per 1000 atoms: 0.38 Number of scatterers: 97374 At special positions: 0 Unit cell: (239.4, 205.8, 257.25, 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 60 16.00 P 3219 15.00 O 27508 8.00 N 18204 7.00 C 48383 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS 2 16 " - pdb=" SG CYS 2 38 " distance=2.29 Simple disulfide: pdb=" SG CYS 4 18 " - pdb=" SG CYS 4 45 " distance=2.65 Simple disulfide: pdb=" SG CYS 7 11 " - pdb=" SG CYS 7 14 " distance=2.02 Simple disulfide: pdb=" SG CYS 7 14 " - pdb=" SG CYS 7 27 " distance=2.00 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 26003 O4' G B 45 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 39.01 Conformation dependent library (CDL) restraints added in 4.6 seconds 7246 Ramachandran restraints generated. 3623 Oldfield, 0 Emsley, 3623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6684 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 51 sheets defined 28.8% alpha, 19.7% beta 1056 base pairs and 1742 stacking pairs defined. Time for finding SS restraints: 34.82 Creating SS restraints... Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.904A pdb=" N LYS C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 226 removed outlier: 3.634A pdb=" N VAL C 225 " --> pdb=" O ARG C 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 Processing helix chain 'D' and resid 88 through 93 Processing helix chain 'D' and resid 102 through 106 removed outlier: 3.711A pdb=" N ILE D 105 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE D 106 " --> pdb=" O ALA D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 102 through 106' Processing helix chain 'D' and resid 125 through 130 Processing helix chain 'E' and resid 23 through 27 removed outlier: 3.955A pdb=" N ASP E 26 " --> pdb=" O GLU E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 43 Processing helix chain 'E' and resid 103 through 121 Processing helix chain 'E' and resid 139 through 148 Processing helix chain 'E' and resid 162 through 170 removed outlier: 3.889A pdb=" N ALA E 166 " --> pdb=" O ASP E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 183 removed outlier: 3.723A pdb=" N LEU E 183 " --> pdb=" O PRO E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 191 Processing helix chain 'E' and resid 198 through 209 Processing helix chain 'F' and resid 9 through 16 Processing helix chain 'F' and resid 17 through 27 Processing helix chain 'F' and resid 55 through 65 removed outlier: 3.701A pdb=" N GLY F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 113 Processing helix chain 'F' and resid 113 through 118 removed outlier: 4.021A pdb=" N ARG F 117 " --> pdb=" O ILE F 113 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE F 118 " --> pdb=" O ALA F 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 113 through 118' Processing helix chain 'F' and resid 170 through 180 Processing helix chain 'G' and resid 59 through 82 removed outlier: 4.227A pdb=" N GLY G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU G 68 " --> pdb=" O SER G 64 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL G 80 " --> pdb=" O LEU G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 151 Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 29 through 34 removed outlier: 3.767A pdb=" N ARG H 33 " --> pdb=" O TYR H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 58 Processing helix chain 'H' and resid 62 through 73 removed outlier: 3.934A pdb=" N ALA H 71 " --> pdb=" O GLU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 107 Processing helix chain 'H' and resid 113 through 117 Processing helix chain 'I' and resid 2 through 19 Processing helix chain 'I' and resid 32 through 43 Processing helix chain 'I' and resid 53 through 61 Processing helix chain 'I' and resid 66 through 70 removed outlier: 3.805A pdb=" N ASP I 70 " --> pdb=" O GLU I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 100 removed outlier: 4.565A pdb=" N ALA I 89 " --> pdb=" O GLU I 85 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA I 90 " --> pdb=" O ALA I 86 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS I 91 " --> pdb=" O VAL I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 124 Processing helix chain 'J' and resid 25 through 31 removed outlier: 3.937A pdb=" N ALA J 29 " --> pdb=" O PRO J 25 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU J 30 " --> pdb=" O VAL J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 49 Processing helix chain 'J' and resid 76 through 81 Processing helix chain 'J' and resid 103 through 114 removed outlier: 3.633A pdb=" N VAL J 107 " --> pdb=" O THR J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 138 removed outlier: 3.943A pdb=" N ALA J 126 " --> pdb=" O ASP J 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 38 Processing helix chain 'K' and resid 58 through 62 removed outlier: 3.945A pdb=" N ILE K 62 " --> pdb=" O ALA K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 72 Processing helix chain 'K' and resid 96 through 109 removed outlier: 4.044A pdb=" N VAL K 100 " --> pdb=" O HIS K 96 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL K 101 " --> pdb=" O PRO K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 118 Processing helix chain 'L' and resid 111 through 118 Processing helix chain 'M' and resid 39 through 44 Processing helix chain 'M' and resid 56 through 61 removed outlier: 3.684A pdb=" N LEU M 61 " --> pdb=" O ILE M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 87 Processing helix chain 'M' and resid 94 through 101 Processing helix chain 'M' and resid 130 through 140 removed outlier: 3.619A pdb=" N ALA M 140 " --> pdb=" O ALA M 136 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 58 removed outlier: 3.612A pdb=" N ILE N 47 " --> pdb=" O THR N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 123 Processing helix chain 'O' and resid 15 through 32 Processing helix chain 'O' and resid 38 through 58 removed outlier: 3.912A pdb=" N ALA O 43 " --> pdb=" O PRO O 39 " (cutoff:3.500A) Proline residue: O 46 - end of helix Processing helix chain 'O' and resid 62 through 67 Processing helix chain 'O' and resid 72 through 87 Proline residue: O 85 - end of helix Processing helix chain 'P' and resid 9 through 24 Processing helix chain 'P' and resid 25 through 28 Processing helix chain 'P' and resid 67 through 72 Processing helix chain 'P' and resid 76 through 95 Processing helix chain 'P' and resid 111 through 123 Processing helix chain 'Q' and resid 4 through 12 removed outlier: 4.836A pdb=" N ALA Q 10 " --> pdb=" O PHE Q 6 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 55 removed outlier: 4.031A pdb=" N SER Q 55 " --> pdb=" O GLY Q 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 52 through 55' Processing helix chain 'Q' and resid 96 through 101 removed outlier: 3.663A pdb=" N LEU Q 99 " --> pdb=" O LEU Q 96 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG Q 100 " --> pdb=" O TYR Q 97 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU Q 101 " --> pdb=" O TYR Q 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 96 through 101' Processing helix chain 'Q' and resid 103 through 108 Processing helix chain 'R' and resid 6 through 21 removed outlier: 4.461A pdb=" N LYS R 13 " --> pdb=" O ASN R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 31 removed outlier: 4.107A pdb=" N ARG R 30 " --> pdb=" O GLY R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 71 removed outlier: 3.681A pdb=" N ARG R 51 " --> pdb=" O TYR R 47 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLY R 55 " --> pdb=" O ARG R 51 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 86 Processing helix chain 'R' and resid 91 through 101 Processing helix chain 'R' and resid 102 through 117 removed outlier: 3.845A pdb=" N PHE R 106 " --> pdb=" O ASP R 102 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU R 117 " --> pdb=" O ALA R 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 57 Processing helix chain 'T' and resid 20 through 32 removed outlier: 4.093A pdb=" N VAL T 27 " --> pdb=" O LYS T 23 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU T 30 " --> pdb=" O ARG T 26 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL T 31 " --> pdb=" O VAL T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 36 through 40 Processing helix chain 'T' and resid 50 through 68 removed outlier: 3.923A pdb=" N VAL T 54 " --> pdb=" O ALA T 50 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 26 removed outlier: 3.756A pdb=" N TYR U 21 " --> pdb=" O SER U 17 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP U 26 " --> pdb=" O GLY U 22 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 50 Processing helix chain 'V' and resid 89 through 92 Processing helix chain 'W' and resid 20 through 30 removed outlier: 3.631A pdb=" N ASP W 30 " --> pdb=" O GLN W 26 " (cutoff:3.500A) Processing helix chain 'W' and resid 51 through 61 Processing helix chain 'W' and resid 160 through 162 No H-bonds generated for 'chain 'W' and resid 160 through 162' Processing helix chain 'W' and resid 186 through 191 Processing helix chain 'Y' and resid 53 through 58 Processing helix chain 'Z' and resid 14 through 39 Processing helix chain 'Z' and resid 44 through 66 Processing helix chain '1' and resid 16 through 27 Processing helix chain '1' and resid 41 through 50 Processing helix chain '2' and resid 42 through 54 removed outlier: 3.522A pdb=" N LYS 2 48 " --> pdb=" O PHE 2 44 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER 2 54 " --> pdb=" O LYS 2 50 " (cutoff:3.500A) Processing helix chain '2' and resid 56 through 65 removed outlier: 3.778A pdb=" N ARG 2 64 " --> pdb=" O ARG 2 60 " (cutoff:3.500A) Processing helix chain '3' and resid 9 through 18 Processing helix chain '3' and resid 43 through 49 Processing helix chain '4' and resid 28 through 32 Processing helix chain '5' and resid 12 through 20 Processing helix chain '5' and resid 20 through 25 Processing helix chain '5' and resid 27 through 40 Processing helix chain '6' and resid 7 through 14 Processing helix chain '6' and resid 37 through 44 Processing helix chain '6' and resid 51 through 63 removed outlier: 4.118A pdb=" N LYS 6 60 " --> pdb=" O SER 6 56 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU 6 61 " --> pdb=" O ARG 6 57 " (cutoff:3.500A) Processing helix chain '8' and resid 3 through 11 Processing helix chain '8' and resid 12 through 14 No H-bonds generated for 'chain '8' and resid 12 through 14' Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'C' and resid 36 through 37 removed outlier: 4.083A pdb=" N LEU C 37 " --> pdb=" O ARG C 60 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ARG C 60 " --> pdb=" O LEU C 37 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 102 through 105 removed outlier: 4.082A pdb=" N HIS C 81 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N HIS C 96 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL C 79 " --> pdb=" O HIS C 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 130 through 132 removed outlier: 5.801A pdb=" N LEU C 165 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG C 176 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLY C 167 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 174 " --> pdb=" O GLY C 167 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR C 172 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG C 184 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE C 268 " --> pdb=" O ARG C 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 174 through 180 removed outlier: 5.811A pdb=" N VAL D 112 " --> pdb=" O ASN D 179 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR D 117 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU D 205 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY D 204 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL D 28 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N MET D 13 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL D 26 " --> pdb=" O MET D 13 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLN D 15 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL D 24 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 191 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL D 185 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU D 193 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 80 through 85 removed outlier: 3.646A pdb=" N ARG D 38 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA D 53 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL D 36 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 123 through 124 Processing sheet with id=AA8, first strand: chain 'E' and resid 16 through 18 removed outlier: 3.546A pdb=" N GLY E 16 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA E 126 " --> pdb=" O ASP E 6 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 97 through 98 removed outlier: 6.957A pdb=" N VAL F 164 " --> pdb=" O VAL F 39 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL F 41 " --> pdb=" O THR F 162 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N THR F 162 " --> pdb=" O VAL F 41 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 73 through 76 removed outlier: 4.159A pdb=" N GLY F 93 " --> pdb=" O ARG F 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 9 through 10 Processing sheet with id=AB3, first strand: chain 'G' and resid 16 through 20 removed outlier: 3.848A pdb=" N GLY G 31 " --> pdb=" O GLY G 28 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 122 through 128 removed outlier: 6.813A pdb=" N LYS G 131 " --> pdb=" O GLU G 127 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 96 through 100 removed outlier: 3.542A pdb=" N GLU G 105 " --> pdb=" O GLN G 98 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN G 103 " --> pdb=" O LYS G 100 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 18 through 20 removed outlier: 3.553A pdb=" N ILE H 37 " --> pdb=" O ILE H 4 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 78 through 81 removed outlier: 6.319A pdb=" N VAL H 78 " --> pdb=" O ASN H 147 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N VAL H 149 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LEU H 80 " --> pdb=" O VAL H 149 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY H 128 " --> pdb=" O VAL H 148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 47 through 51 removed outlier: 6.957A pdb=" N THR I 23 " --> pdb=" O GLY I 108 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY I 108 " --> pdb=" O THR I 23 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL I 25 " --> pdb=" O LYS I 106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 12 through 15 removed outlier: 3.827A pdb=" N LEU J 13 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 101 through 102 removed outlier: 3.544A pdb=" N VAL J 102 " --> pdb=" O THR J 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'K' and resid 54 through 56 Processing sheet with id=AC3, first strand: chain 'K' and resid 73 through 77 removed outlier: 3.526A pdb=" N ARG K 87 " --> pdb=" O ALA K 74 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG K 76 " --> pdb=" O ARG K 85 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG K 85 " --> pdb=" O ARG K 76 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 6 through 9 removed outlier: 3.980A pdb=" N SER L 6 " --> pdb=" O CYS L 21 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP L 45 " --> pdb=" O LYS L 17 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE L 19 " --> pdb=" O VAL L 43 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL L 43 " --> pdb=" O ILE L 19 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N CYS L 21 " --> pdb=" O ALA L 41 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA L 41 " --> pdb=" O CYS L 21 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG L 23 " --> pdb=" O ILE L 39 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE L 39 " --> pdb=" O ARG L 23 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP L 37 " --> pdb=" O VAL L 62 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LYS L 59 " --> pdb=" O ILE L 87 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 76 through 79 removed outlier: 6.661A pdb=" N THR Q 59 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLU Q 63 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N LYS Q 43 " --> pdb=" O GLU Q 63 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASN Q 26 " --> pdb=" O VAL Q 85 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL Q 85 " --> pdb=" O ASN Q 26 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N HIS Q 28 " --> pdb=" O ILE Q 83 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE Q 83 " --> pdb=" O HIS Q 28 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N LYS Q 30 " --> pdb=" O ASP Q 81 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ASP Q 81 " --> pdb=" O LYS Q 30 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 76 through 79 removed outlier: 5.622A pdb=" N GLN M 76 " --> pdb=" O LYS M 111 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LEU M 113 " --> pdb=" O GLN M 76 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL M 78 " --> pdb=" O LEU M 113 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 91 through 93 Processing sheet with id=AC8, first strand: chain 'N' and resid 64 through 66 removed outlier: 6.571A pdb=" N ILE N 34 " --> pdb=" O LEU N 103 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU N 105 " --> pdb=" O TYR N 32 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR N 32 " --> pdb=" O GLU N 105 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 72 through 75 removed outlier: 3.639A pdb=" N LEU N 74 " --> pdb=" O TRP N 92 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TRP N 92 " --> pdb=" O LEU N 74 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 35 through 37 removed outlier: 4.525A pdb=" N MET O 110 " --> pdb=" O VAL O 100 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 58 through 64 removed outlier: 6.378A pdb=" N LEU P 51 " --> pdb=" O LEU P 60 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ALA P 62 " --> pdb=" O VAL P 49 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL P 49 " --> pdb=" O ALA P 62 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER P 64 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE P 47 " --> pdb=" O SER P 64 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'S' and resid 12 through 17 removed outlier: 3.728A pdb=" N ASN S 47 " --> pdb=" O ASP S 44 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 21 through 25 removed outlier: 3.663A pdb=" N GLU S 66 " --> pdb=" O VAL S 96 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LYS S 98 " --> pdb=" O VAL S 64 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N VAL S 64 " --> pdb=" O LYS S 98 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N THR S 100 " --> pdb=" O ALA S 62 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ALA S 62 " --> pdb=" O THR S 100 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 73 through 79 removed outlier: 3.542A pdb=" N LYS S 79 " --> pdb=" O TYR S 84 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR S 84 " --> pdb=" O LYS S 79 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'T' and resid 9 through 17 removed outlier: 5.747A pdb=" N SER T 108 " --> pdb=" O TYR T 16 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS T 34 " --> pdb=" O VAL T 78 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'T' and resid 9 through 17 removed outlier: 5.747A pdb=" N SER T 108 " --> pdb=" O TYR T 16 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N HIS T 109 " --> pdb=" O GLU T 85 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLU T 85 " --> pdb=" O HIS T 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'U' and resid 11 through 14 removed outlier: 3.529A pdb=" N ALA U 13 " --> pdb=" O VAL U 32 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS U 80 " --> pdb=" O VAL U 33 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ARG U 81 " --> pdb=" O THR U 59 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR U 59 " --> pdb=" O ARG U 81 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE U 83 " --> pdb=" O VAL U 57 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL U 57 " --> pdb=" O ILE U 83 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS U 85 " --> pdb=" O ASP U 55 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'V' and resid 66 through 67 removed outlier: 3.634A pdb=" N VAL V 25 " --> pdb=" O LEU V 34 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N THR V 8 " --> pdb=" O VAL V 74 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'V' and resid 40 through 43 Processing sheet with id=AE2, first strand: chain 'V' and resid 84 through 88 removed outlier: 3.826A pdb=" N ASP V 88 " --> pdb=" O LYS V 93 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS V 93 " --> pdb=" O ASP V 88 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'W' and resid 10 through 15 removed outlier: 8.255A pdb=" N THR W 12 " --> pdb=" O ASN W 50 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN W 50 " --> pdb=" O THR W 12 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN W 14 " --> pdb=" O GLU W 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU W 48 " --> pdb=" O ASN W 14 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N ALA W 95 " --> pdb=" O LYS W 32 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N LEU W 97 " --> pdb=" O PRO W 34 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL W 36 " --> pdb=" O LEU W 97 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP W 96 " --> pdb=" O LYS W 81 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN W 76 " --> pdb=" O LEU W 69 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'W' and resid 143 through 149 Processing sheet with id=AE5, first strand: chain 'W' and resid 122 through 126 Processing sheet with id=AE6, first strand: chain 'X' and resid 22 through 23 removed outlier: 6.602A pdb=" N LEU X 59 " --> pdb=" O LEU X 37 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'X' and resid 30 through 31 removed outlier: 6.522A pdb=" N HIS X 46 " --> pdb=" O VAL X 78 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N ILE X 80 " --> pdb=" O HIS X 46 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Y' and resid 13 through 18 removed outlier: 3.548A pdb=" N ARG Y 27 " --> pdb=" O GLY Y 15 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR Y 25 " --> pdb=" O SER Y 17 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Y' and resid 33 through 39 Processing sheet with id=AF1, first strand: chain '1' and resid 34 through 36 Processing sheet with id=AF2, first strand: chain '2' and resid 21 through 26 Processing sheet with id=AF3, first strand: chain '3' and resid 28 through 32 Processing sheet with id=AF4, first strand: chain '4' and resid 22 through 26 Processing sheet with id=AF5, first strand: chain '6' and resid 15 through 17 removed outlier: 3.531A pdb=" N LYS 6 21 " --> pdb=" O THR 6 17 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain '7' and resid 2 through 4 removed outlier: 6.460A pdb=" N LYS 7 2 " --> pdb=" O ARG 7 35 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N VAL 7 23 " --> pdb=" O GLN 7 36 " (cutoff:3.500A) 1011 hydrogen bonds defined for protein. 2835 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2694 hydrogen bonds 4248 hydrogen bond angles 0 basepair planarities 1056 basepair parallelities 1742 stacking parallelities Total time for adding SS restraints: 168.62 Time building geometry restraints manager: 42.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.54: 99304 1.54 - 1.90: 6744 1.90 - 2.25: 0 2.25 - 2.61: 0 2.61 - 2.96: 1 Bond restraints: 106049 Sorted by residual: bond pdb=" C VAL V 47 " pdb=" N SER V 56 " ideal model delta sigma weight residual 1.329 2.960 -1.631 1.40e-02 5.10e+03 1.36e+04 bond pdb=" C ILE W 7 " pdb=" N PRO W 8 " ideal model delta sigma weight residual 1.335 1.389 -0.054 8.70e-03 1.32e+04 3.91e+01 bond pdb=" C ARG T 117 " pdb=" N PRO T 118 " ideal model delta sigma weight residual 1.329 1.397 -0.068 1.18e-02 7.18e+03 3.30e+01 bond pdb=" C ARG O 45 " pdb=" N PRO O 46 " ideal model delta sigma weight residual 1.336 1.403 -0.068 1.23e-02 6.61e+03 3.03e+01 bond pdb=" C ILE F 35 " pdb=" N PRO F 36 " ideal model delta sigma weight residual 1.329 1.389 -0.060 1.20e-02 6.94e+03 2.50e+01 ... (remaining 106044 not shown) Histogram of bond angle deviations from ideal: 71.54 - 86.45: 1 86.45 - 101.35: 1501 101.35 - 116.26: 92910 116.26 - 131.17: 63885 131.17 - 146.07: 1010 Bond angle restraints: 159307 Sorted by residual: angle pdb=" O VAL V 47 " pdb=" C VAL V 47 " pdb=" N SER V 56 " ideal model delta sigma weight residual 121.87 94.18 27.69 9.70e-01 1.06e+00 8.15e+02 angle pdb=" C VAL V 47 " pdb=" N SER V 56 " pdb=" CA SER V 56 " ideal model delta sigma weight residual 121.70 71.54 50.16 1.80e+00 3.09e-01 7.76e+02 angle pdb=" N GLY W 62 " pdb=" CA GLY W 62 " pdb=" C GLY W 62 " ideal model delta sigma weight residual 111.93 133.80 -21.87 1.15e+00 7.56e-01 3.62e+02 angle pdb=" CA VAL V 47 " pdb=" C VAL V 47 " pdb=" N SER V 56 " ideal model delta sigma weight residual 117.15 138.41 -21.26 1.14e+00 7.69e-01 3.48e+02 angle pdb=" N GLY N 61 " pdb=" CA GLY N 61 " pdb=" C GLY N 61 " ideal model delta sigma weight residual 111.36 128.50 -17.14 1.17e+00 7.31e-01 2.15e+02 ... (remaining 159302 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 59409 35.91 - 71.83: 7874 71.83 - 107.74: 890 107.74 - 143.66: 22 143.66 - 179.57: 36 Dihedral angle restraints: 68231 sinusoidal: 57822 harmonic: 10409 Sorted by residual: dihedral pdb=" CA THR D 156 " pdb=" C THR D 156 " pdb=" N PRO D 157 " pdb=" CA PRO D 157 " ideal model delta harmonic sigma weight residual 180.00 92.83 87.17 0 5.00e+00 4.00e-02 3.04e+02 dihedral pdb=" CA ALA X 84 " pdb=" C ALA X 84 " pdb=" N ARG X 85 " pdb=" CA ARG X 85 " ideal model delta harmonic sigma weight residual 180.00 93.84 86.16 0 5.00e+00 4.00e-02 2.97e+02 dihedral pdb=" CA ALA C 144 " pdb=" C ALA C 144 " pdb=" N VAL C 145 " pdb=" CA VAL C 145 " ideal model delta harmonic sigma weight residual 180.00 -132.06 -47.94 0 5.00e+00 4.00e-02 9.19e+01 ... (remaining 68228 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 19963 0.156 - 0.312: 467 0.312 - 0.468: 28 0.468 - 0.624: 4 0.624 - 0.780: 1 Chirality restraints: 20463 Sorted by residual: chirality pdb=" CA PRO T 118 " pdb=" N PRO T 118 " pdb=" C PRO T 118 " pdb=" CB PRO T 118 " both_signs ideal model delta sigma weight residual False 2.72 1.94 0.78 2.00e-01 2.50e+01 1.52e+01 chirality pdb=" CA ARG 5 6 " pdb=" N ARG 5 6 " pdb=" C ARG 5 6 " pdb=" CB ARG 5 6 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.82e+00 chirality pdb=" CA TYR O 87 " pdb=" N TYR O 87 " pdb=" C TYR O 87 " pdb=" CB TYR O 87 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.97e+00 ... (remaining 20460 not shown) Planarity restraints: 8256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL V 47 " -0.086 2.00e-02 2.50e+03 1.11e-01 1.23e+02 pdb=" C VAL V 47 " 0.190 2.00e-02 2.50e+03 pdb=" O VAL V 47 " -0.067 2.00e-02 2.50e+03 pdb=" N SER V 56 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 144 " -0.026 2.00e-02 2.50e+03 5.02e-02 2.52e+01 pdb=" C ALA C 144 " 0.087 2.00e-02 2.50e+03 pdb=" O ALA C 144 " -0.031 2.00e-02 2.50e+03 pdb=" N VAL C 145 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG T 117 " 0.083 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO T 118 " -0.204 5.00e-02 4.00e+02 pdb=" CA PRO T 118 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO T 118 " 0.068 5.00e-02 4.00e+02 ... (remaining 8253 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 129 1.93 - 2.67: 7115 2.67 - 3.42: 116163 3.42 - 4.16: 322381 4.16 - 4.90: 447079 Nonbonded interactions: 892867 Sorted by model distance: nonbonded pdb=" NH1 ARG F 99 " pdb=" C1' G B 45 " model vdw 1.189 3.550 nonbonded pdb=" NE2 GLN K 147 " pdb=" N2 G A1129 " model vdw 1.258 3.200 nonbonded pdb=" O2' U A1598 " pdb=" OP2 U A1599 " model vdw 1.259 2.440 nonbonded pdb=" OE2 GLU F 105 " pdb=" CA ARG 2 25 " model vdw 1.276 3.470 nonbonded pdb=" CE1 TYR W 38 " pdb=" OD1 ASP W 96 " model vdw 1.294 3.340 ... (remaining 892862 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 11.140 Check model and map are aligned: 1.060 Set scattering table: 0.680 Process input model: 347.310 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 366.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 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 : 0.012 1.631 106049 Z= 0.777 Angle : 1.216 50.158 159307 Z= 0.644 Chirality : 0.061 0.780 20463 Planarity : 0.009 0.118 8256 Dihedral : 24.140 179.572 61535 Min Nonbonded Distance : 1.189 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 1.41 % Allowed : 7.87 % Favored : 90.73 % Rotamer: Outliers : 3.90 % Allowed : 6.58 % Favored : 89.51 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.49 % 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: -3.69 (0.12), residues: 3623 helix: -2.74 (0.13), residues: 960 sheet: -1.88 (0.19), residues: 681 loop : -2.53 (0.12), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.006 TRP N 92 HIS 0.026 0.004 HIS T 109 PHE 0.060 0.005 PHE X 69 TYR 0.060 0.005 TYR L 32 ARG 0.031 0.002 ARG X 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7246 Ramachandran restraints generated. 3623 Oldfield, 0 Emsley, 3623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7246 Ramachandran restraints generated. 3623 Oldfield, 0 Emsley, 3623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 933 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 818 time to evaluate : 4.989 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: F 110 LEU cc_start: 0.5219 (OUTLIER) cc_final: 0.4661 (pt) REVERT: I 58 LYS cc_start: 0.2936 (mttt) cc_final: 0.2520 (mmtt) REVERT: K 69 LEU cc_start: 0.7956 (tp) cc_final: 0.7568 (pp) REVERT: K 108 MET cc_start: 0.8378 (mmp) cc_final: 0.8177 (mmp) REVERT: K 147 GLN cc_start: 0.7009 (tm-30) cc_final: 0.6647 (tm-30) REVERT: N 92 TRP cc_start: 0.6052 (OUTLIER) cc_final: 0.4660 (p90) REVERT: Q 54 ILE cc_start: 0.8335 (tt) cc_final: 0.8110 (tt) REVERT: Q 88 ARG cc_start: 0.6416 (mmt180) cc_final: 0.6194 (mtp180) REVERT: Q 100 ARG cc_start: 0.8334 (mtt180) cc_final: 0.8047 (mtt90) REVERT: R 66 ASN cc_start: 0.7443 (t0) cc_final: 0.7241 (t0) REVERT: R 107 THR cc_start: 0.8866 (m) cc_final: 0.8592 (p) REVERT: Y 28 ARG cc_start: 0.7820 (mtm110) cc_final: 0.7509 (mtp85) REVERT: 2 44 PHE cc_start: 0.4053 (OUTLIER) cc_final: 0.3072 (m-80) REVERT: 4 23 TYR cc_start: 0.5508 (OUTLIER) cc_final: 0.4522 (t80) outliers start: 115 outliers final: 36 residues processed: 901 average time/residue: 1.1272 time to fit residues: 1619.8684 Evaluate side-chains 576 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 536 time to evaluate : 3.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 PRO Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain E residue 4 LYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain O residue 16 HIS Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain T residue 6 GLU Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 10 ILE Chi-restraints excluded: chain U residue 75 LYS Chi-restraints excluded: chain U residue 96 PHE Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 96 ARG Chi-restraints excluded: chain W residue 6 ASN Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 40 HIS Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain W residue 101 GLN Chi-restraints excluded: chain W residue 112 VAL Chi-restraints excluded: chain W residue 114 VAL Chi-restraints excluded: chain X residue 15 ASP Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain 1 residue 51 HIS Chi-restraints excluded: chain 2 residue 38 CYS Chi-restraints excluded: chain 2 residue 44 PHE Chi-restraints excluded: chain 4 residue 22 ASN Chi-restraints excluded: chain 4 residue 23 TYR Chi-restraints excluded: chain 4 residue 37 GLU Chi-restraints excluded: chain 4 residue 42 CYS Chi-restraints excluded: chain 5 residue 27 THR Chi-restraints excluded: chain 7 residue 20 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 571 optimal weight: 9.9990 chunk 513 optimal weight: 6.9990 chunk 284 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 346 optimal weight: 10.0000 chunk 274 optimal weight: 1.9990 chunk 530 optimal weight: 0.7980 chunk 205 optimal weight: 2.9990 chunk 322 optimal weight: 10.0000 chunk 394 optimal weight: 0.7980 chunk 614 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 HIS C 96 HIS C 130 ASN C 198 ASN C 227 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 GLN E 35 HIS ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN E 171 ASN E 182 GLN E 202 ASN F 31 ASN ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 GLN ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 GLN H 137 HIS J 33 HIS J 119 ASN K 40 HIS ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 58 ASN K 96 HIS K 117 GLN K 132 HIS ** M 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 GLN N 57 HIS N 96 ASN O 61 HIS O 77 HIS ** P 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 GLN P 56 ASN R 41 HIS R 94 ASN S 85 HIS S 90 HIS ** T 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 34 HIS ** U 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 58 ASN W 46 HIS ** W 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 22 HIS Z 52 GLN ** 1 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 42 GLN 1 48 ASN 1 51 HIS 2 20 HIS 3 36 GLN 4 31 ASN 4 48 HIS 5 11 ASN 5 19 HIS ** 6 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 31 HIS 8 17 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 106049 Z= 0.211 Angle : 0.711 16.005 159307 Z= 0.361 Chirality : 0.039 0.325 20463 Planarity : 0.007 0.174 8256 Dihedral : 24.717 179.963 54671 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.10 % Favored : 93.43 % Rotamer: Outliers : 4.68 % Allowed : 12.35 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 1.21 % Twisted General : 0.17 % 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: -2.63 (0.13), residues: 3625 helix: -1.37 (0.15), residues: 992 sheet: -1.42 (0.18), residues: 748 loop : -2.08 (0.13), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 65 HIS 0.012 0.002 HIS 4 20 PHE 0.033 0.002 PHE E 144 TYR 0.031 0.002 TYR W 38 ARG 0.031 0.001 ARG P 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 641 time to evaluate : 3.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 5 LYS cc_start: 0.8407 (tttt) cc_final: 0.8119 (mtpt) REVERT: E 97 ASP cc_start: 0.6929 (t70) cc_final: 0.6724 (t70) REVERT: E 150 GLU cc_start: 0.3361 (OUTLIER) cc_final: 0.3150 (tp30) REVERT: F 71 LYS cc_start: 0.7855 (tmtm) cc_final: 0.7564 (tttm) REVERT: F 86 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.6291 (tp) REVERT: G 89 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7804 (mt-10) REVERT: G 164 ARG cc_start: 0.7780 (mtt180) cc_final: 0.7542 (mtt90) REVERT: H 105 LYS cc_start: 0.7104 (ttmt) cc_final: 0.6848 (ttmt) REVERT: I 58 LYS cc_start: 0.2594 (mttt) cc_final: 0.2144 (mmtt) REVERT: K 52 ASP cc_start: 0.6460 (m-30) cc_final: 0.6124 (m-30) REVERT: K 75 TYR cc_start: 0.7237 (OUTLIER) cc_final: 0.6982 (m-80) REVERT: K 108 MET cc_start: 0.8307 (mmt) cc_final: 0.7582 (mmt) REVERT: K 132 HIS cc_start: 0.7744 (m-70) cc_final: 0.7531 (m-70) REVERT: N 60 ARG cc_start: 0.5637 (mtt90) cc_final: 0.5217 (mtt90) REVERT: N 91 GLU cc_start: 0.5760 (OUTLIER) cc_final: 0.5021 (pp20) REVERT: N 92 TRP cc_start: 0.5725 (OUTLIER) cc_final: 0.4487 (p90) REVERT: N 122 ILE cc_start: 0.7536 (tt) cc_final: 0.7238 (tt) REVERT: Q 1 MET cc_start: 0.5392 (mmt) cc_final: 0.4582 (mtp) REVERT: Q 38 ARG cc_start: 0.6576 (OUTLIER) cc_final: 0.5310 (ptm160) REVERT: Q 88 ARG cc_start: 0.6687 (mmt180) cc_final: 0.6246 (mtp180) REVERT: Q 100 ARG cc_start: 0.8319 (mtt180) cc_final: 0.7989 (mtt90) REVERT: R 107 THR cc_start: 0.8713 (m) cc_final: 0.8490 (p) REVERT: U 9 ASP cc_start: 0.4706 (OUTLIER) cc_final: 0.4480 (m-30) REVERT: W 83 LEU cc_start: 0.4018 (OUTLIER) cc_final: 0.3559 (mm) REVERT: W 124 VAL cc_start: 0.5928 (m) cc_final: 0.5701 (m) REVERT: 2 13 THR cc_start: 0.7521 (m) cc_final: 0.7307 (t) REVERT: 2 38 CYS cc_start: 0.1701 (OUTLIER) cc_final: 0.1195 (p) REVERT: 3 31 SER cc_start: 0.7931 (OUTLIER) cc_final: 0.7568 (p) REVERT: 3 45 LYS cc_start: 0.8242 (tttm) cc_final: 0.7918 (tttp) REVERT: 4 23 TYR cc_start: 0.5597 (OUTLIER) cc_final: 0.5303 (t80) REVERT: 4 54 SER cc_start: 0.5095 (p) cc_final: 0.4708 (m) REVERT: 6 59 ASN cc_start: 0.7300 (m-40) cc_final: 0.7080 (m-40) outliers start: 138 outliers final: 67 residues processed: 719 average time/residue: 0.9959 time to fit residues: 1181.2870 Evaluate side-chains 618 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 540 time to evaluate : 3.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 130 ASN Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain E residue 4 LYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 91 GLU Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 102 ASN Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 38 ARG Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 45 THR Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 40 HIS Chi-restraints excluded: chain W residue 67 LEU Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 112 VAL Chi-restraints excluded: chain W residue 114 VAL Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain W residue 188 GLU Chi-restraints excluded: chain X residue 15 ASP Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Z residue 25 SER Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 38 CYS Chi-restraints excluded: chain 3 residue 3 VAL Chi-restraints excluded: chain 3 residue 31 SER Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 4 residue 23 TYR Chi-restraints excluded: chain 4 residue 37 GLU Chi-restraints excluded: chain 5 residue 23 LEU Chi-restraints excluded: chain 5 residue 27 THR Chi-restraints excluded: chain 5 residue 45 LEU Chi-restraints excluded: chain 6 residue 34 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 341 optimal weight: 10.0000 chunk 190 optimal weight: 0.9980 chunk 511 optimal weight: 10.0000 chunk 418 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 chunk 615 optimal weight: 10.0000 chunk 665 optimal weight: 5.9990 chunk 548 optimal weight: 8.9990 chunk 610 optimal weight: 8.9990 chunk 209 optimal weight: 0.9990 chunk 494 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 ASN C 122 ASN C 130 ASN C 198 ASN D 34 ASN D 80 HIS ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 GLN F 34 GLN ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 HIS ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 58 ASN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 GLN N 55 ASN ** O 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 48 HIS ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 GLN S 67 HIS S 76 HIS ** T 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 58 ASN W 45 GLN ** W 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 28 ASN 6 35 HIS 7 4 ASN 8 18 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 106049 Z= 0.378 Angle : 0.798 17.920 159307 Z= 0.403 Chirality : 0.044 0.353 20463 Planarity : 0.007 0.158 8256 Dihedral : 24.628 179.989 54634 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.53 % Favored : 92.03 % Rotamer: Outliers : 5.90 % Allowed : 15.51 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 1.21 % Twisted General : 0.17 % 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: -2.29 (0.13), residues: 3625 helix: -0.77 (0.15), residues: 992 sheet: -1.29 (0.19), residues: 736 loop : -2.04 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 206 HIS 0.012 0.002 HIS K 77 PHE 0.026 0.003 PHE E 144 TYR 0.027 0.003 TYR V 27 ARG 0.015 0.001 ARG O 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 576 time to evaluate : 3.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 151 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8270 (tt) REVERT: F 90 MET cc_start: 0.5096 (mtp) cc_final: 0.4729 (mtp) REVERT: I 58 LYS cc_start: 0.2844 (mttt) cc_final: 0.2070 (mmmt) REVERT: K 52 ASP cc_start: 0.6457 (m-30) cc_final: 0.6168 (m-30) REVERT: K 75 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.7168 (m-80) REVERT: L 54 ARG cc_start: 0.6939 (mtm110) cc_final: 0.6588 (mtm180) REVERT: N 12 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7439 (mm110) REVERT: N 17 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7090 (pt0) REVERT: N 91 GLU cc_start: 0.6208 (OUTLIER) cc_final: 0.5692 (pp20) REVERT: N 92 TRP cc_start: 0.6399 (OUTLIER) cc_final: 0.5318 (p90) REVERT: P 20 ARG cc_start: 0.6679 (tpt-90) cc_final: 0.6476 (ttp-110) REVERT: P 109 TYR cc_start: 0.7996 (t80) cc_final: 0.7620 (t80) REVERT: Q 40 GLN cc_start: 0.8278 (tt0) cc_final: 0.8023 (tt0) REVERT: Q 88 ARG cc_start: 0.6669 (mmt180) cc_final: 0.6209 (mtp180) REVERT: R 107 THR cc_start: 0.8700 (m) cc_final: 0.8424 (p) REVERT: S 51 LYS cc_start: 0.6248 (OUTLIER) cc_final: 0.5958 (mptt) REVERT: W 83 LEU cc_start: 0.4039 (OUTLIER) cc_final: 0.3673 (mm) REVERT: X 20 ARG cc_start: 0.8129 (mpt180) cc_final: 0.7919 (mpt180) REVERT: 2 38 CYS cc_start: 0.1489 (OUTLIER) cc_final: 0.1261 (m) REVERT: 2 44 PHE cc_start: 0.3795 (OUTLIER) cc_final: 0.2672 (m-80) REVERT: 3 31 SER cc_start: 0.8032 (p) cc_final: 0.7645 (p) outliers start: 174 outliers final: 105 residues processed: 676 average time/residue: 1.0059 time to fit residues: 1135.6960 Evaluate side-chains 631 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 516 time to evaluate : 3.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 130 ASN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 123 ARG Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 110 MET Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 17 GLN Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 91 GLU Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 102 ASN Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 52 VAL Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain S residue 30 GLU Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 80 ASN Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain T residue 56 LYS Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 90 LYS Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain V residue 45 THR Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 40 HIS Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 112 VAL Chi-restraints excluded: chain W residue 114 VAL Chi-restraints excluded: chain W residue 155 THR Chi-restraints excluded: chain W residue 177 LEU Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain W residue 188 GLU Chi-restraints excluded: chain X residue 15 ASP Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Y residue 33 ILE Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain Z residue 44 ASN Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 2 residue 10 VAL Chi-restraints excluded: chain 2 residue 38 CYS Chi-restraints excluded: chain 2 residue 44 PHE Chi-restraints excluded: chain 3 residue 3 VAL Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 4 residue 23 TYR Chi-restraints excluded: chain 4 residue 37 GLU Chi-restraints excluded: chain 5 residue 27 THR Chi-restraints excluded: chain 6 residue 6 THR Chi-restraints excluded: chain 6 residue 34 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 608 optimal weight: 6.9990 chunk 463 optimal weight: 10.0000 chunk 319 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 293 optimal weight: 8.9990 chunk 413 optimal weight: 7.9990 chunk 618 optimal weight: 7.9990 chunk 654 optimal weight: 10.0000 chunk 322 optimal weight: 10.0000 chunk 585 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 ASN D 51 GLN ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 GLN E 76 GLN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 GLN F 34 GLN G 98 GLN G 103 ASN G 144 GLN H 118 GLN ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 58 ASN ** K 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 132 HIS K 135 GLN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 ASN O 77 HIS ** O 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 HIS ** P 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 GLN T 67 ASN V 44 HIS ** W 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 180 ASN Y 45 ASN 3 12 ASN ** 4 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.118 106049 Z= 0.565 Angle : 0.953 20.179 159307 Z= 0.471 Chirality : 0.052 0.445 20463 Planarity : 0.008 0.148 8256 Dihedral : 24.757 179.952 54623 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.69 % Favored : 90.92 % Rotamer: Outliers : 7.70 % Allowed : 16.69 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 1.21 % Twisted General : 0.14 % 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: -2.51 (0.13), residues: 3625 helix: -0.85 (0.15), residues: 986 sheet: -1.37 (0.18), residues: 743 loop : -2.26 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP N 65 HIS 0.013 0.002 HIS C 231 PHE 0.027 0.003 PHE T 7 TYR 0.031 0.003 TYR N 41 ARG 0.026 0.001 ARG F 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 541 time to evaluate : 3.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 268 ILE cc_start: 0.8840 (mt) cc_final: 0.8616 (mt) REVERT: C 270 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.6830 (tpm-80) REVERT: D 135 GLN cc_start: 0.8357 (mt0) cc_final: 0.8156 (mt0) REVERT: D 151 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8301 (tt) REVERT: E 98 TYR cc_start: 0.7270 (m-80) cc_final: 0.6948 (m-80) REVERT: E 123 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6821 (mtt-85) REVERT: E 139 LYS cc_start: 0.7304 (OUTLIER) cc_final: 0.7043 (ptpp) REVERT: I 79 ILE cc_start: 0.1266 (OUTLIER) cc_final: 0.1018 (pt) REVERT: J 137 MET cc_start: 0.4738 (mmt) cc_final: 0.4366 (mmt) REVERT: K 75 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.6909 (m-80) REVERT: K 135 GLN cc_start: 0.6581 (OUTLIER) cc_final: 0.5408 (mm110) REVERT: L 54 ARG cc_start: 0.6955 (mtm110) cc_final: 0.6642 (mtm180) REVERT: M 127 ASN cc_start: 0.8528 (t0) cc_final: 0.8253 (t0) REVERT: N 12 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7631 (mt0) REVERT: N 60 ARG cc_start: 0.6121 (OUTLIER) cc_final: 0.5648 (mtt90) REVERT: N 122 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7677 (tt) REVERT: P 20 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6421 (ttp-110) REVERT: P 109 TYR cc_start: 0.8022 (t80) cc_final: 0.7647 (t80) REVERT: Q 88 ARG cc_start: 0.6856 (mmt180) cc_final: 0.6390 (mtp180) REVERT: R 107 THR cc_start: 0.8607 (m) cc_final: 0.8360 (p) REVERT: T 37 GLU cc_start: 0.4520 (OUTLIER) cc_final: 0.4315 (mp0) REVERT: U 24 ILE cc_start: 0.8790 (mm) cc_final: 0.8468 (mt) REVERT: W 181 VAL cc_start: 0.7360 (OUTLIER) cc_final: 0.6855 (p) REVERT: X 73 ARG cc_start: 0.7079 (ptp90) cc_final: 0.6861 (ptp90) REVERT: X 85 ARG cc_start: 0.5360 (OUTLIER) cc_final: 0.4943 (ttm170) REVERT: Y 39 VAL cc_start: 0.8020 (OUTLIER) cc_final: 0.7767 (m) REVERT: Y 54 SER cc_start: 0.8044 (t) cc_final: 0.7663 (p) REVERT: 2 10 VAL cc_start: 0.4796 (OUTLIER) cc_final: 0.4585 (p) REVERT: 2 11 ASP cc_start: 0.6547 (OUTLIER) cc_final: 0.5638 (p0) REVERT: 2 44 PHE cc_start: 0.4218 (OUTLIER) cc_final: 0.1823 (m-80) REVERT: 3 31 SER cc_start: 0.7970 (p) cc_final: 0.7583 (p) REVERT: 6 57 ARG cc_start: 0.7991 (ttt90) cc_final: 0.7787 (ttt-90) outliers start: 227 outliers final: 155 residues processed: 689 average time/residue: 0.9567 time to fit residues: 1108.1675 Evaluate side-chains 675 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 502 time to evaluate : 3.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 130 ASN Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 123 ARG Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 58 ASN Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain K residue 135 GLN Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 59 MET Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 39 HIS Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 60 ARG Chi-restraints excluded: chain N residue 71 ASP Chi-restraints excluded: chain N residue 91 GLU Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 102 ASN Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 10 ILE Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 52 VAL Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain S residue 30 GLU Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 80 ASN Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 37 GLU Chi-restraints excluded: chain T residue 56 LYS Chi-restraints excluded: chain T residue 78 VAL Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 90 LYS Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 36 ASP Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 93 ILE Chi-restraints excluded: chain V residue 45 THR Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 40 HIS Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 114 VAL Chi-restraints excluded: chain W residue 122 THR Chi-restraints excluded: chain W residue 124 VAL Chi-restraints excluded: chain W residue 155 THR Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain W residue 188 GLU Chi-restraints excluded: chain X residue 15 ASP Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain X residue 85 ARG Chi-restraints excluded: chain Y residue 33 ILE Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain Z residue 25 SER Chi-restraints excluded: chain Z residue 43 ASN Chi-restraints excluded: chain Z residue 44 ASN Chi-restraints excluded: chain Z residue 54 ILE Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 2 residue 10 VAL Chi-restraints excluded: chain 2 residue 11 ASP Chi-restraints excluded: chain 2 residue 44 PHE Chi-restraints excluded: chain 3 residue 3 VAL Chi-restraints excluded: chain 3 residue 29 THR Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 4 residue 37 GLU Chi-restraints excluded: chain 4 residue 38 ILE Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 27 THR Chi-restraints excluded: chain 6 residue 6 THR Chi-restraints excluded: chain 6 residue 12 LYS Chi-restraints excluded: chain 6 residue 23 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 545 optimal weight: 7.9990 chunk 371 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 487 optimal weight: 50.0000 chunk 270 optimal weight: 6.9990 chunk 558 optimal weight: 5.9990 chunk 452 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 334 optimal weight: 8.9990 chunk 587 optimal weight: 4.9990 chunk 165 optimal weight: 0.5980 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 ASN D 135 GLN E 83 GLN E 121 ASN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 GLN ** E 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 ASN ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 58 ASN K 132 HIS ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 HIS P 86 GLN ** W 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 161 GLN ** 1 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 106049 Z= 0.303 Angle : 0.723 16.338 159307 Z= 0.364 Chirality : 0.041 0.362 20463 Planarity : 0.006 0.151 8256 Dihedral : 24.594 179.733 54617 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.81 % Favored : 91.81 % Rotamer: Outliers : 6.48 % Allowed : 19.00 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 1.82 % Twisted General : 0.11 % 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: -2.16 (0.13), residues: 3625 helix: -0.36 (0.16), residues: 988 sheet: -1.36 (0.18), residues: 731 loop : -2.07 (0.13), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 214 HIS 0.009 0.002 HIS 4 20 PHE 0.015 0.002 PHE E 144 TYR 0.021 0.002 TYR N 41 ARG 0.013 0.001 ARG F 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 530 time to evaluate : 3.888 Fit side-chains revert: symmetry clash REVERT: C 222 ARG cc_start: 0.7626 (ptt-90) cc_final: 0.7312 (ptt90) REVERT: E 139 LYS cc_start: 0.7125 (OUTLIER) cc_final: 0.6902 (ptpp) REVERT: E 196 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7629 (m-10) REVERT: F 84 PHE cc_start: 0.6376 (OUTLIER) cc_final: 0.4625 (m-80) REVERT: I 79 ILE cc_start: 0.1323 (OUTLIER) cc_final: 0.1074 (pt) REVERT: J 137 MET cc_start: 0.4672 (mmt) cc_final: 0.4428 (mmt) REVERT: K 75 TYR cc_start: 0.7903 (OUTLIER) cc_final: 0.6943 (m-80) REVERT: K 135 GLN cc_start: 0.6297 (OUTLIER) cc_final: 0.6006 (mm-40) REVERT: N 17 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7361 (pt0) REVERT: N 60 ARG cc_start: 0.6079 (OUTLIER) cc_final: 0.5287 (mtt90) REVERT: N 91 GLU cc_start: 0.6230 (OUTLIER) cc_final: 0.4995 (pp20) REVERT: N 122 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7602 (tt) REVERT: P 20 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6476 (ttp-110) REVERT: Q 88 ARG cc_start: 0.6823 (mmt180) cc_final: 0.6327 (mtp180) REVERT: R 107 THR cc_start: 0.8557 (m) cc_final: 0.8312 (p) REVERT: T 16 TYR cc_start: 0.7575 (m-80) cc_final: 0.7349 (m-80) REVERT: T 37 GLU cc_start: 0.4546 (OUTLIER) cc_final: 0.4327 (mp0) REVERT: W 181 VAL cc_start: 0.7317 (OUTLIER) cc_final: 0.6966 (p) REVERT: X 15 ASP cc_start: 0.6979 (OUTLIER) cc_final: 0.6707 (p0) REVERT: Y 39 VAL cc_start: 0.8051 (OUTLIER) cc_final: 0.7809 (m) REVERT: Y 54 SER cc_start: 0.7929 (t) cc_final: 0.7561 (p) REVERT: 2 8 GLU cc_start: 0.6730 (tm-30) cc_final: 0.6481 (tm-30) REVERT: 2 11 ASP cc_start: 0.6479 (OUTLIER) cc_final: 0.5804 (p0) REVERT: 2 44 PHE cc_start: 0.3925 (OUTLIER) cc_final: 0.2168 (m-80) REVERT: 3 31 SER cc_start: 0.7976 (p) cc_final: 0.7600 (p) REVERT: 4 37 GLU cc_start: 0.6288 (OUTLIER) cc_final: 0.5663 (pp20) outliers start: 191 outliers final: 133 residues processed: 646 average time/residue: 0.9465 time to fit residues: 1027.0626 Evaluate side-chains 657 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 506 time to evaluate : 3.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 130 ASN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 182 GLN Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 103 ASN Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain K residue 119 GLN Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 135 GLN Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 17 GLN Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 60 ARG Chi-restraints excluded: chain N residue 71 ASP Chi-restraints excluded: chain N residue 91 GLU Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 102 ASN Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain S residue 30 GLU Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 80 ASN Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 37 GLU Chi-restraints excluded: chain T residue 56 LYS Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 90 LYS Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 84 VAL Chi-restraints excluded: chain U residue 90 SER Chi-restraints excluded: chain V residue 13 SER Chi-restraints excluded: chain V residue 45 THR Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 40 HIS Chi-restraints excluded: chain W residue 67 LEU Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 114 VAL Chi-restraints excluded: chain W residue 122 THR Chi-restraints excluded: chain W residue 124 VAL Chi-restraints excluded: chain W residue 176 LEU Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain W residue 188 GLU Chi-restraints excluded: chain X residue 15 ASP Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain Z residue 43 ASN Chi-restraints excluded: chain 2 residue 11 ASP Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 44 PHE Chi-restraints excluded: chain 2 residue 58 VAL Chi-restraints excluded: chain 3 residue 3 VAL Chi-restraints excluded: chain 3 residue 32 VAL Chi-restraints excluded: chain 4 residue 37 GLU Chi-restraints excluded: chain 5 residue 27 THR Chi-restraints excluded: chain 6 residue 6 THR Chi-restraints excluded: chain 6 residue 12 LYS Chi-restraints excluded: chain 6 residue 23 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 220 optimal weight: 0.8980 chunk 589 optimal weight: 10.0000 chunk 129 optimal weight: 0.7980 chunk 384 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 655 optimal weight: 4.9990 chunk 543 optimal weight: 10.0000 chunk 303 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 343 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 ASN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 GLN E 184 ASN ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 HIS N 67 ASN P 8 GLN ** P 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 86 GLN ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 50 ASN 4 31 ASN ** 4 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 106049 Z= 0.208 Angle : 0.633 14.406 159307 Z= 0.321 Chirality : 0.036 0.339 20463 Planarity : 0.006 0.148 8256 Dihedral : 24.475 179.817 54611 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.98 % Favored : 92.69 % Rotamer: Outliers : 5.53 % Allowed : 20.87 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 2.42 % Twisted General : 0.11 % 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: -1.82 (0.14), residues: 3625 helix: 0.02 (0.16), residues: 990 sheet: -1.11 (0.19), residues: 736 loop : -1.95 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 214 HIS 0.023 0.001 HIS N 13 PHE 0.016 0.001 PHE M 87 TYR 0.015 0.002 TYR N 41 ARG 0.020 0.001 ARG V 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 536 time to evaluate : 4.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 226 MET cc_start: 0.7917 (mtt) cc_final: 0.7712 (mtt) REVERT: C 270 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6857 (tpm-80) REVERT: F 84 PHE cc_start: 0.6088 (OUTLIER) cc_final: 0.4264 (m-80) REVERT: H 101 VAL cc_start: 0.6480 (t) cc_final: 0.6197 (m) REVERT: I 79 ILE cc_start: 0.1306 (OUTLIER) cc_final: 0.1078 (pt) REVERT: J 137 MET cc_start: 0.4800 (mmt) cc_final: 0.4536 (mmt) REVERT: K 75 TYR cc_start: 0.7789 (OUTLIER) cc_final: 0.6895 (m-80) REVERT: L 120 GLU cc_start: 0.7523 (tp30) cc_final: 0.7265 (tm-30) REVERT: M 127 ASN cc_start: 0.8239 (t0) cc_final: 0.7937 (t0) REVERT: N 60 ARG cc_start: 0.5979 (OUTLIER) cc_final: 0.5013 (mtt90) REVERT: N 91 GLU cc_start: 0.5810 (OUTLIER) cc_final: 0.4967 (pp20) REVERT: P 20 ARG cc_start: 0.7105 (tpt-90) cc_final: 0.6457 (ttp-110) REVERT: P 83 ARG cc_start: 0.6956 (mmm160) cc_final: 0.6729 (tpt170) REVERT: Q 88 ARG cc_start: 0.6791 (mmt180) cc_final: 0.6361 (mtp180) REVERT: T 91 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7707 (mtt-85) REVERT: X 15 ASP cc_start: 0.6893 (OUTLIER) cc_final: 0.6628 (p0) REVERT: Y 39 VAL cc_start: 0.8062 (OUTLIER) cc_final: 0.7809 (m) REVERT: Y 54 SER cc_start: 0.7776 (t) cc_final: 0.7426 (p) REVERT: Z 35 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7985 (mp10) REVERT: 2 11 ASP cc_start: 0.6350 (OUTLIER) cc_final: 0.5735 (p0) REVERT: 2 44 PHE cc_start: 0.3690 (OUTLIER) cc_final: 0.2077 (m-80) REVERT: 3 6 ARG cc_start: 0.7940 (mpt-90) cc_final: 0.7740 (mmt180) REVERT: 3 31 SER cc_start: 0.8056 (p) cc_final: 0.7700 (p) REVERT: 4 37 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.5996 (pp20) outliers start: 163 outliers final: 108 residues processed: 636 average time/residue: 0.9768 time to fit residues: 1041.8337 Evaluate side-chains 623 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 502 time to evaluate : 3.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 130 ASN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 60 ARG Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 GLU Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 102 ASN Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain S residue 30 GLU Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 56 LYS Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 90 LYS Chi-restraints excluded: chain T residue 91 ARG Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 36 ASP Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain V residue 13 SER Chi-restraints excluded: chain V residue 45 THR Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 40 HIS Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 114 VAL Chi-restraints excluded: chain W residue 122 THR Chi-restraints excluded: chain W residue 124 VAL Chi-restraints excluded: chain W residue 155 THR Chi-restraints excluded: chain W residue 176 LEU Chi-restraints excluded: chain W residue 179 VAL Chi-restraints excluded: chain W residue 188 GLU Chi-restraints excluded: chain X residue 15 ASP Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain Z residue 35 GLN Chi-restraints excluded: chain Z residue 43 ASN Chi-restraints excluded: chain 2 residue 11 ASP Chi-restraints excluded: chain 2 residue 44 PHE Chi-restraints excluded: chain 2 residue 58 VAL Chi-restraints excluded: chain 3 residue 3 VAL Chi-restraints excluded: chain 3 residue 32 VAL Chi-restraints excluded: chain 4 residue 31 ASN Chi-restraints excluded: chain 4 residue 37 GLU Chi-restraints excluded: chain 5 residue 27 THR Chi-restraints excluded: chain 6 residue 12 LYS Chi-restraints excluded: chain 6 residue 23 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 631 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 373 optimal weight: 20.0000 chunk 478 optimal weight: 10.0000 chunk 370 optimal weight: 10.0000 chunk 551 optimal weight: 8.9990 chunk 365 optimal weight: 9.9990 chunk 652 optimal weight: 6.9990 chunk 408 optimal weight: 7.9990 chunk 397 optimal weight: 10.0000 chunk 301 optimal weight: 4.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 ASN C 227 ASN D 145 HIS E 83 GLN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 ASN ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 GLN N 67 ASN O 17 GLN O 61 HIS ** P 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 86 GLN S 88 GLN ** T 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 31 ASN ** 4 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 34 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 106049 Z= 0.489 Angle : 0.884 17.224 159307 Z= 0.437 Chirality : 0.048 0.340 20463 Planarity : 0.007 0.146 8256 Dihedral : 24.582 179.421 54609 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.30 % Favored : 90.32 % Rotamer: Outliers : 7.30 % Allowed : 20.43 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 2.42 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.13), residues: 3625 helix: -0.37 (0.16), residues: 982 sheet: -1.32 (0.18), residues: 740 loop : -2.20 (0.13), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 214 HIS 0.011 0.002 HIS 4 20 PHE 0.024 0.003 PHE O 80 TYR 0.032 0.003 TYR N 41 ARG 0.009 0.001 ARG 4 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 512 time to evaluate : 3.928 Fit side-chains REVERT: C 148 ARG cc_start: 0.7829 (mtp85) cc_final: 0.7626 (mtp85) REVERT: C 270 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6883 (tpm-80) REVERT: C 273 ARG cc_start: 0.6944 (tmt170) cc_final: 0.6451 (ttt180) REVERT: D 142 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7598 (tt0) REVERT: E 129 GLU cc_start: 0.6149 (OUTLIER) cc_final: 0.5279 (tp30) REVERT: F 84 PHE cc_start: 0.6612 (OUTLIER) cc_final: 0.4614 (m-80) REVERT: H 135 LYS cc_start: 0.6845 (ttmm) cc_final: 0.6548 (tttp) REVERT: J 137 MET cc_start: 0.4763 (mmt) cc_final: 0.4554 (mmt) REVERT: K 75 TYR cc_start: 0.7912 (OUTLIER) cc_final: 0.6959 (m-80) REVERT: L 120 GLU cc_start: 0.7666 (tp30) cc_final: 0.7339 (tm-30) REVERT: M 57 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8203 (tp) REVERT: M 127 ASN cc_start: 0.8474 (t0) cc_final: 0.8250 (t0) REVERT: N 51 ARG cc_start: 0.7770 (tmm160) cc_final: 0.7529 (ttp80) REVERT: N 60 ARG cc_start: 0.6302 (OUTLIER) cc_final: 0.5231 (mtt90) REVERT: N 91 GLU cc_start: 0.6283 (OUTLIER) cc_final: 0.4762 (pp20) REVERT: P 20 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6377 (ttp-110) REVERT: Q 88 ARG cc_start: 0.7064 (mmt180) cc_final: 0.6635 (mtp180) REVERT: T 37 GLU cc_start: 0.4660 (OUTLIER) cc_final: 0.4365 (mp0) REVERT: T 91 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7670 (mtt-85) REVERT: U 66 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6467 (ptm-80) REVERT: W 58 LEU cc_start: 0.5445 (tp) cc_final: 0.5189 (tp) REVERT: W 181 VAL cc_start: 0.7490 (OUTLIER) cc_final: 0.7101 (p) REVERT: X 15 ASP cc_start: 0.7021 (OUTLIER) cc_final: 0.6769 (p0) REVERT: Y 39 VAL cc_start: 0.8115 (OUTLIER) cc_final: 0.7877 (m) REVERT: Y 54 SER cc_start: 0.7988 (t) cc_final: 0.7620 (p) REVERT: 2 11 ASP cc_start: 0.6670 (OUTLIER) cc_final: 0.6106 (p0) REVERT: 2 44 PHE cc_start: 0.3875 (OUTLIER) cc_final: 0.1374 (m-80) outliers start: 215 outliers final: 162 residues processed: 650 average time/residue: 0.9566 time to fit residues: 1056.6506 Evaluate side-chains 678 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 499 time to evaluate : 3.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 130 ASN Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 142 GLN Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 39 HIS Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 60 ARG Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 71 ASP Chi-restraints excluded: chain N residue 91 GLU Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 102 ASN Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 10 ILE Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 52 VAL Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain S residue 30 GLU Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 50 SER Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 80 ASN Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 37 GLU Chi-restraints excluded: chain T residue 38 GLU Chi-restraints excluded: chain T residue 56 LYS Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 90 LYS Chi-restraints excluded: chain T residue 91 ARG Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 36 ASP Chi-restraints excluded: chain U residue 51 ASP Chi-restraints excluded: chain U residue 66 ARG Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 90 SER Chi-restraints excluded: chain U residue 93 ILE Chi-restraints excluded: chain U residue 96 PHE Chi-restraints excluded: chain V residue 13 SER Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 45 THR Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 40 HIS Chi-restraints excluded: chain W residue 67 LEU Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 98 LEU Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 114 VAL Chi-restraints excluded: chain W residue 122 THR Chi-restraints excluded: chain W residue 124 VAL Chi-restraints excluded: chain W residue 155 THR Chi-restraints excluded: chain W residue 176 LEU Chi-restraints excluded: chain W residue 179 VAL Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain W residue 188 GLU Chi-restraints excluded: chain X residue 15 ASP Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Y residue 33 ILE Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain Z residue 36 MET Chi-restraints excluded: chain Z residue 43 ASN Chi-restraints excluded: chain Z residue 44 ASN Chi-restraints excluded: chain Z residue 54 ILE Chi-restraints excluded: chain 1 residue 31 ILE Chi-restraints excluded: chain 2 residue 11 ASP Chi-restraints excluded: chain 2 residue 44 PHE Chi-restraints excluded: chain 2 residue 58 VAL Chi-restraints excluded: chain 3 residue 3 VAL Chi-restraints excluded: chain 3 residue 32 VAL Chi-restraints excluded: chain 4 residue 37 GLU Chi-restraints excluded: chain 5 residue 27 THR Chi-restraints excluded: chain 6 residue 6 THR Chi-restraints excluded: chain 6 residue 12 LYS Chi-restraints excluded: chain 6 residue 23 VAL Chi-restraints excluded: chain 6 residue 34 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 403 optimal weight: 10.0000 chunk 260 optimal weight: 0.9980 chunk 389 optimal weight: 5.9990 chunk 196 optimal weight: 0.1980 chunk 128 optimal weight: 0.4980 chunk 126 optimal weight: 6.9990 chunk 414 optimal weight: 5.9990 chunk 444 optimal weight: 10.0000 chunk 322 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 512 optimal weight: 7.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 ASN E 83 GLN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 130 HIS ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 14 HIS N 67 ASN O 17 GLN ** P 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 86 GLN ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 31 ASN 4 51 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 106049 Z= 0.191 Angle : 0.629 13.288 159307 Z= 0.319 Chirality : 0.036 0.328 20463 Planarity : 0.005 0.081 8256 Dihedral : 24.461 179.789 54609 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.95 % Favored : 92.74 % Rotamer: Outliers : 5.43 % Allowed : 22.36 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 2.42 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.14), residues: 3625 helix: 0.15 (0.17), residues: 968 sheet: -1.16 (0.18), residues: 780 loop : -1.96 (0.14), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 214 HIS 0.008 0.001 HIS C 245 PHE 0.018 0.001 PHE P 127 TYR 0.021 0.002 TYR P 109 ARG 0.011 0.001 ARG P 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 522 time to evaluate : 4.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 270 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.6822 (tpm-80) REVERT: E 73 ARG cc_start: 0.7753 (mtp-110) cc_final: 0.7240 (mtp85) REVERT: E 129 GLU cc_start: 0.5865 (OUTLIER) cc_final: 0.5142 (tp30) REVERT: F 26 GLU cc_start: 0.6112 (tt0) cc_final: 0.5875 (tt0) REVERT: F 84 PHE cc_start: 0.6128 (OUTLIER) cc_final: 0.4216 (m-80) REVERT: H 101 VAL cc_start: 0.6488 (t) cc_final: 0.6195 (m) REVERT: H 135 LYS cc_start: 0.6880 (ttmm) cc_final: 0.6671 (tttp) REVERT: K 10 ASP cc_start: 0.7081 (p0) cc_final: 0.6731 (p0) REVERT: K 75 TYR cc_start: 0.7771 (OUTLIER) cc_final: 0.6884 (m-80) REVERT: L 120 GLU cc_start: 0.7448 (tp30) cc_final: 0.7094 (tm-30) REVERT: M 127 ASN cc_start: 0.8286 (t0) cc_final: 0.8008 (t0) REVERT: N 60 ARG cc_start: 0.6105 (OUTLIER) cc_final: 0.4829 (mtt90) REVERT: N 91 GLU cc_start: 0.5849 (OUTLIER) cc_final: 0.5049 (pp20) REVERT: P 20 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6448 (ttp-110) REVERT: P 83 ARG cc_start: 0.6803 (mmm160) cc_final: 0.6581 (tpt170) REVERT: Q 88 ARG cc_start: 0.7002 (mmt180) cc_final: 0.6558 (mtp180) REVERT: T 91 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7705 (mtt-85) REVERT: W 83 LEU cc_start: 0.4047 (OUTLIER) cc_final: 0.3586 (mm) REVERT: W 188 GLU cc_start: 0.4181 (OUTLIER) cc_final: 0.3205 (tm-30) REVERT: X 15 ASP cc_start: 0.6921 (OUTLIER) cc_final: 0.6670 (p0) REVERT: Y 39 VAL cc_start: 0.8151 (OUTLIER) cc_final: 0.7934 (m) REVERT: Y 54 SER cc_start: 0.7771 (t) cc_final: 0.7428 (p) REVERT: Z 35 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.8010 (mp10) REVERT: 2 8 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6795 (tm-30) REVERT: 2 11 ASP cc_start: 0.6522 (OUTLIER) cc_final: 0.6159 (p0) REVERT: 2 44 PHE cc_start: 0.3633 (OUTLIER) cc_final: 0.1721 (m-80) outliers start: 160 outliers final: 119 residues processed: 611 average time/residue: 0.9850 time to fit residues: 1018.1283 Evaluate side-chains 635 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 501 time to evaluate : 3.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 130 ASN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain K residue 119 GLN Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 14 HIS Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 60 ARG Chi-restraints excluded: chain N residue 71 ASP Chi-restraints excluded: chain N residue 91 GLU Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 102 ASN Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 29 SER Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain S residue 30 GLU Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 56 LYS Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 90 LYS Chi-restraints excluded: chain T residue 91 ARG Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 51 ASP Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 90 SER Chi-restraints excluded: chain U residue 96 PHE Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 40 HIS Chi-restraints excluded: chain W residue 67 LEU Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 98 LEU Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 114 VAL Chi-restraints excluded: chain W residue 122 THR Chi-restraints excluded: chain W residue 124 VAL Chi-restraints excluded: chain W residue 155 THR Chi-restraints excluded: chain W residue 176 LEU Chi-restraints excluded: chain W residue 179 VAL Chi-restraints excluded: chain W residue 188 GLU Chi-restraints excluded: chain X residue 15 ASP Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain X residue 57 ASP Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain Z residue 35 GLN Chi-restraints excluded: chain 1 residue 31 ILE Chi-restraints excluded: chain 2 residue 11 ASP Chi-restraints excluded: chain 2 residue 44 PHE Chi-restraints excluded: chain 2 residue 58 VAL Chi-restraints excluded: chain 3 residue 3 VAL Chi-restraints excluded: chain 3 residue 32 VAL Chi-restraints excluded: chain 4 residue 37 GLU Chi-restraints excluded: chain 5 residue 27 THR Chi-restraints excluded: chain 6 residue 6 THR Chi-restraints excluded: chain 6 residue 12 LYS Chi-restraints excluded: chain 6 residue 23 VAL Chi-restraints excluded: chain 7 residue 19 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 593 optimal weight: 10.0000 chunk 625 optimal weight: 10.0000 chunk 570 optimal weight: 10.0000 chunk 608 optimal weight: 8.9990 chunk 624 optimal weight: 10.0000 chunk 365 optimal weight: 10.0000 chunk 264 optimal weight: 0.1980 chunk 477 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 549 optimal weight: 8.9990 chunk 575 optimal weight: 8.9990 overall best weight: 7.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 ASN E 83 GLN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 GLN ** E 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 GLN ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** M 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 67 ASN O 17 GLN ** P 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 86 GLN ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 88 GLN ** T 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 34 HIS ** W 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 42 GLN 4 31 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.117 106049 Z= 0.549 Angle : 0.925 16.812 159307 Z= 0.455 Chirality : 0.050 0.351 20463 Planarity : 0.008 0.088 8256 Dihedral : 24.614 179.641 54609 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.85 % Favored : 89.77 % Rotamer: Outliers : 5.97 % Allowed : 22.57 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 2.42 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.13), residues: 3625 helix: -0.40 (0.16), residues: 984 sheet: -1.41 (0.18), residues: 749 loop : -2.31 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 214 HIS 0.014 0.002 HIS D 145 PHE 0.025 0.003 PHE T 7 TYR 0.037 0.003 TYR K 4 ARG 0.009 0.001 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 522 time to evaluate : 3.962 Fit side-chains revert: symmetry clash REVERT: C 268 ILE cc_start: 0.8832 (mt) cc_final: 0.8521 (mt) REVERT: C 270 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6830 (tpm-80) REVERT: C 273 ARG cc_start: 0.6969 (tmt170) cc_final: 0.6592 (ttt180) REVERT: E 129 GLU cc_start: 0.6155 (OUTLIER) cc_final: 0.5281 (tp30) REVERT: F 84 PHE cc_start: 0.6615 (OUTLIER) cc_final: 0.4848 (m-80) REVERT: G 166 GLU cc_start: 0.7198 (tp30) cc_final: 0.6825 (tp30) REVERT: H 2 LYS cc_start: 0.7019 (mtmm) cc_final: 0.6703 (mtmt) REVERT: H 135 LYS cc_start: 0.6887 (ttmm) cc_final: 0.6630 (tttp) REVERT: K 10 ASP cc_start: 0.7357 (p0) cc_final: 0.7137 (p0) REVERT: K 75 TYR cc_start: 0.7959 (OUTLIER) cc_final: 0.7027 (m-80) REVERT: L 120 GLU cc_start: 0.7619 (tp30) cc_final: 0.7259 (tm-30) REVERT: M 127 ASN cc_start: 0.8525 (t0) cc_final: 0.8312 (t0) REVERT: N 12 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7396 (mm110) REVERT: N 51 ARG cc_start: 0.7801 (tmm160) cc_final: 0.7572 (ttp80) REVERT: N 60 ARG cc_start: 0.6428 (OUTLIER) cc_final: 0.5163 (mtt90) REVERT: N 91 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.5084 (pp20) REVERT: P 20 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6314 (ttp-110) REVERT: Q 88 ARG cc_start: 0.7239 (mmt180) cc_final: 0.6782 (mtp180) REVERT: T 91 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7602 (mtt-85) REVERT: W 58 LEU cc_start: 0.5521 (tp) cc_final: 0.5271 (tp) REVERT: W 181 VAL cc_start: 0.7444 (OUTLIER) cc_final: 0.7047 (p) REVERT: W 188 GLU cc_start: 0.4221 (OUTLIER) cc_final: 0.3362 (tm-30) REVERT: X 15 ASP cc_start: 0.6976 (OUTLIER) cc_final: 0.6690 (p0) REVERT: Y 39 VAL cc_start: 0.8272 (OUTLIER) cc_final: 0.8053 (m) REVERT: Y 54 SER cc_start: 0.8028 (t) cc_final: 0.7646 (p) REVERT: 2 8 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6946 (tm-30) REVERT: 2 11 ASP cc_start: 0.6658 (OUTLIER) cc_final: 0.6190 (p0) REVERT: 2 44 PHE cc_start: 0.4030 (OUTLIER) cc_final: 0.1632 (m-80) REVERT: 3 37 ARG cc_start: 0.7875 (mtt90) cc_final: 0.7564 (mtp180) outliers start: 176 outliers final: 141 residues processed: 630 average time/residue: 0.9686 time to fit residues: 1027.9401 Evaluate side-chains 658 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 502 time to evaluate : 3.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 130 ASN Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain K residue 95 LYS Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain K residue 119 GLN Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 14 HIS Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 60 ARG Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 71 ASP Chi-restraints excluded: chain N residue 91 GLU Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 102 ASN Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 10 ILE Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain S residue 30 GLU Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 50 SER Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 80 ASN Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 56 LYS Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 90 LYS Chi-restraints excluded: chain T residue 91 ARG Chi-restraints excluded: chain U residue 6 ASP Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 51 ASP Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 90 SER Chi-restraints excluded: chain U residue 96 PHE Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 45 THR Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 40 HIS Chi-restraints excluded: chain W residue 42 THR Chi-restraints excluded: chain W residue 67 LEU Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 98 LEU Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 114 VAL Chi-restraints excluded: chain W residue 122 THR Chi-restraints excluded: chain W residue 124 VAL Chi-restraints excluded: chain W residue 155 THR Chi-restraints excluded: chain W residue 176 LEU Chi-restraints excluded: chain W residue 179 VAL Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain W residue 188 GLU Chi-restraints excluded: chain X residue 15 ASP Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain Z residue 44 ASN Chi-restraints excluded: chain Z residue 54 ILE Chi-restraints excluded: chain 1 residue 31 ILE Chi-restraints excluded: chain 2 residue 11 ASP Chi-restraints excluded: chain 2 residue 44 PHE Chi-restraints excluded: chain 2 residue 58 VAL Chi-restraints excluded: chain 3 residue 3 VAL Chi-restraints excluded: chain 3 residue 32 VAL Chi-restraints excluded: chain 4 residue 31 ASN Chi-restraints excluded: chain 4 residue 37 GLU Chi-restraints excluded: chain 5 residue 27 THR Chi-restraints excluded: chain 6 residue 6 THR Chi-restraints excluded: chain 6 residue 12 LYS Chi-restraints excluded: chain 6 residue 23 VAL Chi-restraints excluded: chain 6 residue 34 GLU Chi-restraints excluded: chain 7 residue 19 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 605 optimal weight: 4.9990 chunk 399 optimal weight: 7.9990 chunk 642 optimal weight: 1.9990 chunk 392 optimal weight: 9.9990 chunk 305 optimal weight: 0.7980 chunk 446 optimal weight: 20.0000 chunk 674 optimal weight: 1.9990 chunk 620 optimal weight: 4.9990 chunk 537 optimal weight: 30.0000 chunk 55 optimal weight: 0.9990 chunk 414 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 GLN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 HIS ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** M 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 67 ASN ** P 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 86 GLN ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 88 GLN ** T 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 31 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.177 106049 Z= 0.320 Angle : 0.895 59.200 159307 Z= 0.453 Chirality : 0.044 0.342 20463 Planarity : 0.007 0.099 8256 Dihedral : 24.619 179.708 54607 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.93 % Favored : 89.68 % Rotamer: Outliers : 5.63 % Allowed : 22.90 % Favored : 71.46 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 2.42 % Twisted General : 0.11 % 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: -2.38 (0.13), residues: 3625 helix: -0.37 (0.16), residues: 984 sheet: -1.47 (0.18), residues: 749 loop : -2.33 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 214 HIS 0.031 0.002 HIS N 14 PHE 0.024 0.002 PHE T 7 TYR 0.032 0.003 TYR N 41 ARG 0.017 0.001 ARG O 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 508 time to evaluate : 3.957 Fit side-chains revert: symmetry clash REVERT: C 237 GLU cc_start: 0.7713 (tm-30) cc_final: 0.6931 (tm-30) REVERT: C 268 ILE cc_start: 0.8810 (mt) cc_final: 0.8497 (mt) REVERT: C 270 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6787 (tpm-80) REVERT: C 273 ARG cc_start: 0.6940 (tmt170) cc_final: 0.6497 (ttt180) REVERT: D 142 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: E 129 GLU cc_start: 0.6153 (OUTLIER) cc_final: 0.5258 (tp30) REVERT: F 84 PHE cc_start: 0.6583 (OUTLIER) cc_final: 0.4834 (m-80) REVERT: G 166 GLU cc_start: 0.7183 (tp30) cc_final: 0.6813 (tp30) REVERT: H 135 LYS cc_start: 0.6895 (ttmm) cc_final: 0.6646 (tttp) REVERT: K 1 MET cc_start: 0.5228 (ttt) cc_final: 0.4965 (ttt) REVERT: K 10 ASP cc_start: 0.7336 (p0) cc_final: 0.7108 (p0) REVERT: K 75 TYR cc_start: 0.7910 (OUTLIER) cc_final: 0.7008 (m-80) REVERT: L 120 GLU cc_start: 0.7586 (tp30) cc_final: 0.7241 (tm-30) REVERT: M 127 ASN cc_start: 0.8436 (t0) cc_final: 0.8224 (t0) REVERT: N 12 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7328 (mm110) REVERT: N 51 ARG cc_start: 0.7749 (tmm160) cc_final: 0.7518 (ttp80) REVERT: N 60 ARG cc_start: 0.6490 (OUTLIER) cc_final: 0.5127 (mtt90) REVERT: N 91 GLU cc_start: 0.6299 (OUTLIER) cc_final: 0.4787 (pp20) REVERT: P 20 ARG cc_start: 0.6972 (OUTLIER) cc_final: 0.6297 (ttp-110) REVERT: Q 38 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.5473 (ptm160) REVERT: Q 88 ARG cc_start: 0.7283 (mmt180) cc_final: 0.6769 (mtp180) REVERT: T 91 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7610 (mtt-85) REVERT: W 181 VAL cc_start: 0.7429 (OUTLIER) cc_final: 0.7049 (p) REVERT: W 188 GLU cc_start: 0.4213 (OUTLIER) cc_final: 0.3351 (tm-30) REVERT: X 15 ASP cc_start: 0.6961 (OUTLIER) cc_final: 0.6702 (p0) REVERT: Y 39 VAL cc_start: 0.8142 (OUTLIER) cc_final: 0.7940 (m) REVERT: Y 54 SER cc_start: 0.7996 (t) cc_final: 0.7612 (p) REVERT: 2 8 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6949 (tm-30) REVERT: 2 11 ASP cc_start: 0.6622 (OUTLIER) cc_final: 0.6178 (p0) REVERT: 2 44 PHE cc_start: 0.3969 (OUTLIER) cc_final: 0.1604 (m-80) REVERT: 3 37 ARG cc_start: 0.7893 (mtt90) cc_final: 0.7549 (mtp180) outliers start: 166 outliers final: 145 residues processed: 606 average time/residue: 0.9728 time to fit residues: 990.7946 Evaluate side-chains 669 residues out of total 2973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 507 time to evaluate : 3.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 142 GLN Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain K residue 119 GLN Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 60 ARG Chi-restraints excluded: chain N residue 71 ASP Chi-restraints excluded: chain N residue 91 GLU Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 101 GLU Chi-restraints excluded: chain O residue 102 ASN Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain P residue 10 ILE Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain Q residue 23 ASP Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 38 ARG Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 27 GLN Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain S residue 30 GLU Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 50 SER Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 80 ASN Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 56 LYS Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 90 LYS Chi-restraints excluded: chain T residue 91 ARG Chi-restraints excluded: chain U residue 6 ASP Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 51 ASP Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 90 SER Chi-restraints excluded: chain U residue 96 PHE Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 45 THR Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 40 HIS Chi-restraints excluded: chain W residue 42 THR Chi-restraints excluded: chain W residue 67 LEU Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 98 LEU Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 114 VAL Chi-restraints excluded: chain W residue 122 THR Chi-restraints excluded: chain W residue 124 VAL Chi-restraints excluded: chain W residue 155 THR Chi-restraints excluded: chain W residue 176 LEU Chi-restraints excluded: chain W residue 179 VAL Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain W residue 188 GLU Chi-restraints excluded: chain X residue 15 ASP Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain X residue 57 ASP Chi-restraints excluded: chain Y residue 33 ILE Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain Z residue 44 ASN Chi-restraints excluded: chain Z residue 54 ILE Chi-restraints excluded: chain 1 residue 31 ILE Chi-restraints excluded: chain 2 residue 11 ASP Chi-restraints excluded: chain 2 residue 44 PHE Chi-restraints excluded: chain 2 residue 58 VAL Chi-restraints excluded: chain 3 residue 3 VAL Chi-restraints excluded: chain 3 residue 32 VAL Chi-restraints excluded: chain 4 residue 31 ASN Chi-restraints excluded: chain 4 residue 37 GLU Chi-restraints excluded: chain 5 residue 27 THR Chi-restraints excluded: chain 5 residue 36 ASN Chi-restraints excluded: chain 6 residue 6 THR Chi-restraints excluded: chain 6 residue 12 LYS Chi-restraints excluded: chain 6 residue 23 VAL Chi-restraints excluded: chain 6 residue 34 GLU Chi-restraints excluded: chain 7 residue 19 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 329 optimal weight: 9.9990 chunk 426 optimal weight: 9.9990 chunk 572 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 495 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 537 optimal weight: 30.0000 chunk 225 optimal weight: 4.9990 chunk 552 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 67 ASN ** P 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 86 GLN ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 88 GLN ** T 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.204018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.173420 restraints weight = 129053.222| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 0.94 r_work: 0.3724 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.242 106049 Z= 0.322 Angle : 0.882 26.425 159307 Z= 0.446 Chirality : 0.044 0.342 20463 Planarity : 0.007 0.099 8256 Dihedral : 24.619 179.708 54607 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.93 % Favored : 89.68 % Rotamer: Outliers : 5.46 % Allowed : 23.04 % Favored : 71.50 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 2.42 % Twisted General : 0.11 % 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: -2.38 (0.13), residues: 3625 helix: -0.37 (0.16), residues: 984 sheet: -1.47 (0.18), residues: 749 loop : -2.33 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 214 HIS 0.031 0.002 HIS N 14 PHE 0.024 0.002 PHE T 7 TYR 0.032 0.003 TYR N 41 ARG 0.017 0.001 ARG O 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19333.14 seconds wall clock time: 343 minutes 56.97 seconds (20636.97 seconds total)