Starting phenix.real_space_refine on Thu Feb 22 11:22:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afo_11772/02_2024/7afo_11772_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afo_11772/02_2024/7afo_11772.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afo_11772/02_2024/7afo_11772_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afo_11772/02_2024/7afo_11772_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afo_11772/02_2024/7afo_11772_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afo_11772/02_2024/7afo_11772.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afo_11772/02_2024/7afo_11772.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afo_11772/02_2024/7afo_11772_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afo_11772/02_2024/7afo_11772_neut_updated.pdb" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 971 5.49 5 Mg 20 5.21 5 S 59 5.16 5 C 17608 2.51 5 N 6333 2.21 5 O 9143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34134 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 20869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 20869 Classifications: {'RNA': 971} Modifications used: {'rna2p': 2, 'rna2p_pur': 76, 'rna2p_pyr': 52, 'rna3p': 1, 'rna3p_pur': 484, 'rna3p_pyr': 356} Link IDs: {'rna2p': 129, 'rna3p': 841} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1144 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 430 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "X" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1174 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "Y" Number of atoms: 1963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1963 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 19, 'TRANS': 232} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Unusual residues: {' MG': 20} Classifications: {'undetermined': 20} Link IDs: {None: 19} Time building chain proxies: 18.77, per 1000 atoms: 0.55 Number of scatterers: 34134 At special positions: 0 Unit cell: (124.775, 158.41, 218.085, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 59 16.00 P 971 15.00 Mg 20 11.99 O 9143 8.00 N 6333 7.00 C 17608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 24.53 Conformation dependent library (CDL) restraints added in 2.8 seconds 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3150 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 16 sheets defined 39.3% alpha, 16.7% beta 339 base pairs and 482 stacking pairs defined. Time for finding SS restraints: 19.89 Creating SS restraints... Processing helix chain 'D' and resid 9 through 14 Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 40 through 43 removed outlier: 3.692A pdb=" N ALA D 43 " --> pdb=" O GLN D 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 40 through 43' Processing helix chain 'D' and resid 50 through 65 Processing helix chain 'D' and resid 69 through 81 Processing helix chain 'D' and resid 86 through 95 Processing helix chain 'D' and resid 98 through 105 Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 147 through 150 No H-bonds generated for 'chain 'D' and resid 147 through 150' Processing helix chain 'D' and resid 153 through 164 removed outlier: 4.215A pdb=" N GLU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 190 No H-bonds generated for 'chain 'D' and resid 188 through 190' Processing helix chain 'D' and resid 197 through 205 removed outlier: 4.662A pdb=" N LEU D 203 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TYR D 204 " --> pdb=" O ILE D 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 68 Processing helix chain 'E' and resid 109 through 118 removed outlier: 3.959A pdb=" N ALA E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 145 Processing helix chain 'E' and resid 150 through 156 Processing helix chain 'E' and resid 158 through 163 Processing helix chain 'F' and resid 12 through 32 removed outlier: 5.614A pdb=" N GLU F 16 " --> pdb=" O ASP F 13 " (cutoff:3.500A) Proline residue: F 19 - end of helix removed outlier: 3.654A pdb=" N TYR F 25 " --> pdb=" O ILE F 22 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA F 27 " --> pdb=" O ARG F 24 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR F 30 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY F 31 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 80 removed outlier: 3.516A pdb=" N ARG F 79 " --> pdb=" O GLU F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 104 No H-bonds generated for 'chain 'F' and resid 101 through 104' Processing helix chain 'H' and resid 6 through 19 Processing helix chain 'H' and resid 31 through 42 Processing helix chain 'H' and resid 95 through 98 Processing helix chain 'H' and resid 113 through 119 removed outlier: 3.700A pdb=" N GLN H 118 " --> pdb=" O ARG H 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 50 No H-bonds generated for 'chain 'K' and resid 47 through 50' Processing helix chain 'K' and resid 54 through 58 Processing helix chain 'K' and resid 60 through 77 removed outlier: 3.622A pdb=" N GLU K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 101 Processing helix chain 'L' and resid 4 through 9 Processing helix chain 'L' and resid 22 through 24 No H-bonds generated for 'chain 'L' and resid 22 through 24' Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 25 through 45 removed outlier: 4.302A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU O 45 " --> pdb=" O GLY O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 73 removed outlier: 4.056A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 84 Processing helix chain 'P' and resid 54 through 62 Processing helix chain 'P' and resid 69 through 81 Processing helix chain 'Q' and resid 49 through 51 No H-bonds generated for 'chain 'Q' and resid 49 through 51' Processing helix chain 'R' and resid 11 through 19 Processing helix chain 'R' and resid 26 through 32 removed outlier: 4.066A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TYR R 32 " --> pdb=" O THR R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 45 No H-bonds generated for 'chain 'R' and resid 42 through 45' Processing helix chain 'R' and resid 49 through 64 Processing helix chain 'T' and resid 5 through 40 removed outlier: 3.862A pdb=" N SER T 23 " --> pdb=" O LYS T 19 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG T 24 " --> pdb=" O HIS T 20 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS T 34 " --> pdb=" O THR T 30 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 63 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 69 through 85 Processing helix chain 'U' and resid 12 through 26 Processing helix chain 'U' and resid 28 through 36 removed outlier: 3.533A pdb=" N GLU U 36 " --> pdb=" O VAL U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 60 removed outlier: 4.585A pdb=" N LYS U 58 " --> pdb=" O LYS U 54 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS U 59 " --> pdb=" O ARG U 55 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU U 60 " --> pdb=" O HIS U 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 18 Proline residue: X 15 - end of helix Processing helix chain 'X' and resid 48 through 61 Processing helix chain 'X' and resid 63 through 65 No H-bonds generated for 'chain 'X' and resid 63 through 65' Processing helix chain 'X' and resid 88 through 94 removed outlier: 3.540A pdb=" N PHE X 94 " --> pdb=" O HIS X 90 " (cutoff:3.500A) Processing helix chain 'X' and resid 129 through 131 No H-bonds generated for 'chain 'X' and resid 129 through 131' Processing helix chain 'Y' and resid 23 through 33 Processing helix chain 'Y' and resid 49 through 58 Proline residue: Y 54 - end of helix Processing helix chain 'Y' and resid 69 through 76 Processing helix chain 'Y' and resid 92 through 94 No H-bonds generated for 'chain 'Y' and resid 92 through 94' Processing helix chain 'Y' and resid 97 through 103 Processing helix chain 'Y' and resid 117 through 129 removed outlier: 3.887A pdb=" N THR Y 120 " --> pdb=" O ASN Y 117 " (cutoff:3.500A) Proline residue: Y 121 - end of helix Processing helix chain 'Y' and resid 142 through 148 Processing helix chain 'Y' and resid 159 through 167 Processing helix chain 'Y' and resid 178 through 180 No H-bonds generated for 'chain 'Y' and resid 178 through 180' Processing helix chain 'Y' and resid 207 through 220 Processing helix chain 'Y' and resid 225 through 227 No H-bonds generated for 'chain 'Y' and resid 225 through 227' Processing helix chain 'Y' and resid 229 through 231 No H-bonds generated for 'chain 'Y' and resid 229 through 231' Processing helix chain 'Y' and resid 235 through 240 Processing helix chain 'Y' and resid 249 through 251 No H-bonds generated for 'chain 'Y' and resid 249 through 251' Processing helix chain 'Y' and resid 254 through 267 Processing sheet with id= A, first strand: chain 'D' and resid 123 through 125 removed outlier: 3.973A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 46 through 53 removed outlier: 3.511A pdb=" N GLY E 51 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 86 through 89 Processing sheet with id= D, first strand: chain 'F' and resid 84 through 90 removed outlier: 6.919A pdb=" N MET F 9 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER F 87 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL F 7 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL F 89 " --> pdb=" O GLU F 5 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLU F 5 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG F 38 " --> pdb=" O ASN F 63 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.687A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 75 through 77 removed outlier: 6.644A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'K' and resid 83 through 87 Processing sheet with id= H, first strand: chain 'L' and resid 30 through 33 Processing sheet with id= I, first strand: chain 'L' and resid 36 through 40 Processing sheet with id= J, first strand: chain 'P' and resid 2 through 11 removed outlier: 6.861A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'Q' and resid 73 through 75 removed outlier: 8.097A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'Q' and resid 58 through 60 removed outlier: 5.653A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N VAL Q 78 " --> pdb=" O GLU Q 60 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'X' and resid 72 through 77 removed outlier: 6.356A pdb=" N SER X 34 " --> pdb=" O ASN X 73 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N GLU X 75 " --> pdb=" O SER X 34 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU X 36 " --> pdb=" O GLU X 75 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N SER X 77 " --> pdb=" O LEU X 36 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE X 38 " --> pdb=" O SER X 77 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASP X 41 " --> pdb=" O LEU X 23 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LEU X 23 " --> pdb=" O ASP X 41 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'X' and resid 112 through 116 Processing sheet with id= O, first strand: chain 'X' and resid 134 through 137 Processing sheet with id= P, first strand: chain 'Y' and resid 85 through 89 removed outlier: 6.574A pdb=" N LEU Y 62 " --> pdb=" O THR Y 86 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N TYR Y 88 " --> pdb=" O LEU Y 62 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL Y 64 " --> pdb=" O TYR Y 88 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL Y 110 " --> pdb=" O ALA Y 134 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N MET Y 136 " --> pdb=" O VAL Y 110 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N GLY Y 112 " --> pdb=" O MET Y 136 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N PHE Y 138 " --> pdb=" O GLY Y 112 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA Y 134 " --> pdb=" O PRO Y 196 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ARG Y 193 " --> pdb=" O PRO Y 172 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL Y 195 " --> pdb=" O VAL Y 170 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL Y 170 " --> pdb=" O VAL Y 195 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1491 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 851 hydrogen bonds 1342 hydrogen bond angles 0 basepair planarities 339 basepair parallelities 482 stacking parallelities Total time for adding SS restraints: 22.54 Time building geometry restraints manager: 25.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 3107 1.29 - 1.42: 15994 1.42 - 1.56: 15675 1.56 - 1.69: 1940 1.69 - 1.82: 103 Bond restraints: 36819 Sorted by residual: bond pdb=" N3 2MG A1516 " pdb=" C4 2MG A1516 " ideal model delta sigma weight residual 1.496 1.345 0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" C2 2MG A1516 " pdb=" N2 2MG A1516 " ideal model delta sigma weight residual 1.475 1.339 0.136 2.00e-02 2.50e+03 4.65e+01 bond pdb=" C5 MA6 A1519 " pdb=" C4 MA6 A1519 " ideal model delta sigma weight residual 1.342 1.471 -0.129 2.00e-02 2.50e+03 4.16e+01 bond pdb=" C LEU Y 229 " pdb=" O LEU Y 229 " ideal model delta sigma weight residual 1.236 1.154 0.082 1.29e-02 6.01e+03 4.03e+01 bond pdb=" C5 MA6 A1518 " pdb=" C4 MA6 A1518 " ideal model delta sigma weight residual 1.342 1.467 -0.125 2.00e-02 2.50e+03 3.90e+01 ... (remaining 36814 not shown) Histogram of bond angle deviations from ideal: 92.39 - 101.26: 1451 101.26 - 110.13: 15419 110.13 - 119.00: 20198 119.00 - 127.87: 15883 127.87 - 136.75: 1611 Bond angle restraints: 54562 Sorted by residual: angle pdb=" CA GLY E 108 " pdb=" C GLY E 108 " pdb=" O GLY E 108 " ideal model delta sigma weight residual 121.58 113.99 7.59 9.00e-01 1.23e+00 7.12e+01 angle pdb=" C5' A A 819 " pdb=" C4' A A 819 " pdb=" C3' A A 819 " ideal model delta sigma weight residual 115.20 102.57 12.63 1.50e+00 4.44e-01 7.09e+01 angle pdb=" C5' A A 816 " pdb=" C4' A A 816 " pdb=" C3' A A 816 " ideal model delta sigma weight residual 116.00 103.78 12.22 1.50e+00 4.44e-01 6.64e+01 angle pdb=" O3' A A 196 " pdb=" P A A 197 " pdb=" O5' A A 197 " ideal model delta sigma weight residual 104.00 92.39 11.61 1.50e+00 4.44e-01 5.99e+01 angle pdb=" N ASN X 109 " pdb=" CA ASN X 109 " pdb=" C ASN X 109 " ideal model delta sigma weight residual 111.28 101.11 10.17 1.35e+00 5.49e-01 5.68e+01 ... (remaining 54557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 21118 35.90 - 71.81: 2158 71.81 - 107.71: 202 107.71 - 143.62: 16 143.62 - 179.52: 5 Dihedral angle restraints: 23499 sinusoidal: 18628 harmonic: 4871 Sorted by residual: dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 59.40 140.60 1 1.50e+01 4.44e-03 7.56e+01 dihedral pdb=" O4' C A 754 " pdb=" C1' C A 754 " pdb=" N1 C A 754 " pdb=" C2 C A 754 " ideal model delta sinusoidal sigma weight residual 200.00 60.09 139.91 1 1.50e+01 4.44e-03 7.53e+01 dihedral pdb=" O4' U A 85 " pdb=" C1' U A 85 " pdb=" N1 U A 85 " pdb=" C2 U A 85 " ideal model delta sinusoidal sigma weight residual 232.00 52.48 179.52 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 23496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 4942 0.100 - 0.199: 1636 0.199 - 0.299: 284 0.299 - 0.399: 24 0.399 - 0.499: 4 Chirality restraints: 6890 Sorted by residual: chirality pdb=" CA TYR Y 116 " pdb=" N TYR Y 116 " pdb=" C TYR Y 116 " pdb=" CB TYR Y 116 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.22e+00 chirality pdb=" CA ARG X 110 " pdb=" N ARG X 110 " pdb=" C ARG X 110 " pdb=" CB ARG X 110 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.09e+00 chirality pdb=" CA GLN T 55 " pdb=" N GLN T 55 " pdb=" C GLN T 55 " pdb=" CB GLN T 55 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.47e+00 ... (remaining 6887 not shown) Planarity restraints: 3327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " 0.103 2.00e-02 2.50e+03 3.18e-01 2.28e+03 pdb=" C4' 2MG A1516 " -0.349 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " -0.217 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " 0.491 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " -0.040 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " 0.409 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " -0.377 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " -0.310 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " 0.289 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 844 " 0.284 2.00e-02 2.50e+03 1.60e-01 7.71e+02 pdb=" N9 G A 844 " 0.021 2.00e-02 2.50e+03 pdb=" C8 G A 844 " -0.261 2.00e-02 2.50e+03 pdb=" N7 G A 844 " -0.193 2.00e-02 2.50e+03 pdb=" C5 G A 844 " 0.016 2.00e-02 2.50e+03 pdb=" C6 G A 844 " 0.119 2.00e-02 2.50e+03 pdb=" O6 G A 844 " 0.126 2.00e-02 2.50e+03 pdb=" N1 G A 844 " 0.138 2.00e-02 2.50e+03 pdb=" C2 G A 844 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G A 844 " -0.268 2.00e-02 2.50e+03 pdb=" N3 G A 844 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G A 844 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 346 " 0.306 2.00e-02 2.50e+03 1.39e-01 5.81e+02 pdb=" N9 G A 346 " -0.012 2.00e-02 2.50e+03 pdb=" C8 G A 346 " -0.118 2.00e-02 2.50e+03 pdb=" N7 G A 346 " -0.137 2.00e-02 2.50e+03 pdb=" C5 G A 346 " -0.102 2.00e-02 2.50e+03 pdb=" C6 G A 346 " 0.024 2.00e-02 2.50e+03 pdb=" O6 G A 346 " 0.282 2.00e-02 2.50e+03 pdb=" N1 G A 346 " -0.016 2.00e-02 2.50e+03 pdb=" C2 G A 346 " -0.038 2.00e-02 2.50e+03 pdb=" N2 G A 346 " -0.040 2.00e-02 2.50e+03 pdb=" N3 G A 346 " -0.051 2.00e-02 2.50e+03 pdb=" C4 G A 346 " -0.098 2.00e-02 2.50e+03 ... (remaining 3324 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 28 2.47 - 3.07: 22827 3.07 - 3.68: 73332 3.68 - 4.29: 98168 4.29 - 4.90: 133896 Nonbonded interactions: 328251 Sorted by model distance: nonbonded pdb=" OP1 G A 558 " pdb="MG MG A1610 " model vdw 1.857 2.170 nonbonded pdb=" OP2 A A 573 " pdb="MG MG A1614 " model vdw 1.882 2.170 nonbonded pdb=" OP1 G A 21 " pdb="MG MG A1604 " model vdw 1.883 2.170 nonbonded pdb=" OP2 U A 398 " pdb="MG MG A1611 " model vdw 1.891 2.170 nonbonded pdb=" OP1 A A 174 " pdb="MG MG A1609 " model vdw 1.900 2.170 ... (remaining 328246 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 13.660 Check model and map are aligned: 0.600 Set scattering table: 0.370 Process input model: 121.960 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 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 : 0.014 0.151 36819 Z= 0.843 Angle : 1.972 17.184 54562 Z= 1.269 Chirality : 0.097 0.499 6890 Planarity : 0.035 0.318 3327 Dihedral : 23.049 179.519 20349 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.71 % Allowed : 8.91 % Favored : 90.38 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.19), residues: 1660 helix: -1.55 (0.17), residues: 690 sheet: -0.31 (0.34), residues: 203 loop : -1.21 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.025 TRP X 113 HIS 0.016 0.004 HIS Y 137 PHE 0.084 0.013 PHE X 136 TYR 0.210 0.029 TYR Y 157 ARG 0.016 0.002 ARG P 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 502 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 TYR cc_start: 0.7761 (t80) cc_final: 0.7359 (t80) REVERT: D 51 TYR cc_start: 0.9479 (t80) cc_final: 0.8966 (t80) REVERT: D 71 GLN cc_start: 0.9123 (mt0) cc_final: 0.8755 (mt0) REVERT: D 74 ASN cc_start: 0.9306 (m-40) cc_final: 0.8553 (m-40) REVERT: D 75 TYR cc_start: 0.9308 (m-80) cc_final: 0.8972 (m-80) REVERT: D 76 TYR cc_start: 0.9548 (t80) cc_final: 0.9277 (t80) REVERT: D 77 LYS cc_start: 0.9612 (mtmt) cc_final: 0.9332 (mtmm) REVERT: D 132 ILE cc_start: 0.9305 (mm) cc_final: 0.9053 (mm) REVERT: D 178 MET cc_start: 0.8322 (mtm) cc_final: 0.8081 (mtm) REVERT: D 182 PHE cc_start: 0.9504 (t80) cc_final: 0.9029 (t80) REVERT: D 196 ASN cc_start: 0.8969 (m-40) cc_final: 0.8539 (m110) REVERT: E 30 ILE cc_start: 0.8082 (mm) cc_final: 0.7753 (mm) REVERT: E 54 ARG cc_start: 0.9072 (mmm160) cc_final: 0.8796 (mpt180) REVERT: E 64 MET cc_start: 0.9288 (mmt) cc_final: 0.8982 (mmm) REVERT: E 72 ILE cc_start: 0.9409 (pt) cc_final: 0.9184 (tp) REVERT: E 134 ILE cc_start: 0.9709 (pt) cc_final: 0.9452 (mm) REVERT: E 141 ILE cc_start: 0.9818 (mm) cc_final: 0.9602 (mm) REVERT: E 156 LYS cc_start: 0.8779 (mtmt) cc_final: 0.8538 (mmtt) REVERT: F 6 ILE cc_start: 0.9423 (mt) cc_final: 0.9191 (mm) REVERT: F 8 PHE cc_start: 0.9589 (p90) cc_final: 0.9332 (p90) REVERT: F 62 MET cc_start: 0.8961 (mtp) cc_final: 0.8414 (mpp) REVERT: F 79 ARG cc_start: 0.8858 (ptp90) cc_final: 0.8429 (mpp80) REVERT: F 88 MET cc_start: 0.9026 (ttm) cc_final: 0.8805 (ttm) REVERT: F 92 THR cc_start: 0.8920 (p) cc_final: 0.8252 (p) REVERT: H 11 LEU cc_start: 0.9795 (mt) cc_final: 0.9492 (mt) REVERT: H 27 MET cc_start: 0.9099 (mpp) cc_final: 0.8631 (mpp) REVERT: H 38 ASN cc_start: 0.9613 (t0) cc_final: 0.8726 (t0) REVERT: H 43 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8703 (tp30) REVERT: H 85 ILE cc_start: 0.9452 (mm) cc_final: 0.9121 (mm) REVERT: H 86 TYR cc_start: 0.8363 (m-80) cc_final: 0.7692 (m-10) REVERT: H 90 ASP cc_start: 0.9645 (p0) cc_final: 0.9432 (p0) REVERT: H 124 GLU cc_start: 0.9043 (tt0) cc_final: 0.8404 (tt0) REVERT: K 33 THR cc_start: 0.8554 (p) cc_final: 0.8060 (p) REVERT: L 5 ASN cc_start: 0.9535 (t0) cc_final: 0.8958 (t0) REVERT: L 35 THR cc_start: 0.9425 (p) cc_final: 0.9065 (p) REVERT: L 55 VAL cc_start: 0.9588 (OUTLIER) cc_final: 0.9372 (p) REVERT: L 73 ASN cc_start: 0.8241 (p0) cc_final: 0.7845 (p0) REVERT: L 103 ASP cc_start: 0.9117 (t0) cc_final: 0.8531 (t0) REVERT: O 68 ASP cc_start: 0.9253 (m-30) cc_final: 0.9049 (m-30) REVERT: P 18 GLN cc_start: 0.9339 (mm-40) cc_final: 0.9004 (mm110) REVERT: P 26 ASN cc_start: 0.9068 (m110) cc_final: 0.8777 (m110) REVERT: Q 38 ILE cc_start: 0.9761 (pt) cc_final: 0.9548 (mm) REVERT: Q 80 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8117 (tm-30) REVERT: R 60 LYS cc_start: 0.9703 (mttt) cc_final: 0.9423 (mtpt) REVERT: T 13 GLN cc_start: 0.9509 (pt0) cc_final: 0.9041 (pp30) REVERT: U 23 CYS cc_start: 0.8908 (p) cc_final: 0.8607 (p) REVERT: U 35 ARG cc_start: 0.9051 (ttm170) cc_final: 0.8827 (mtt180) REVERT: U 36 GLU cc_start: 0.9699 (tp30) cc_final: 0.9270 (tp30) REVERT: U 42 THR cc_start: 0.8851 (t) cc_final: 0.8567 (m) REVERT: X 101 LEU cc_start: 0.9391 (mp) cc_final: 0.8847 (tp) REVERT: Y 136 MET cc_start: 0.8662 (mpt) cc_final: 0.8454 (mpt) REVERT: Y 137 HIS cc_start: 0.8588 (m90) cc_final: 0.8243 (m170) REVERT: Y 155 LYS cc_start: 0.8564 (tppp) cc_final: 0.8046 (tppt) REVERT: Y 159 ARG cc_start: 0.9057 (tmt170) cc_final: 0.8716 (tmm-80) REVERT: Y 163 MET cc_start: 0.9699 (mmm) cc_final: 0.9063 (mmm) REVERT: Y 202 HIS cc_start: 0.9302 (m90) cc_final: 0.9026 (m90) REVERT: Y 222 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8407 (mmm-85) REVERT: Y 241 MET cc_start: 0.9124 (mmm) cc_final: 0.8732 (mmt) REVERT: Y 247 MET cc_start: 0.8947 (mtm) cc_final: 0.8660 (mpp) outliers start: 10 outliers final: 2 residues processed: 508 average time/residue: 0.6245 time to fit residues: 463.2379 Evaluate side-chains 354 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 350 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 222 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 5.9990 chunk 197 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 203 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 123 optimal weight: 7.9990 chunk 151 optimal weight: 10.0000 chunk 236 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN E 97 GLN E 146 ASN ** F 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 HIS T 84 ASN U 56 HIS Y 34 ASN Y 113 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36819 Z= 0.184 Angle : 0.731 12.701 54562 Z= 0.385 Chirality : 0.041 0.343 6890 Planarity : 0.006 0.110 3327 Dihedral : 23.872 177.749 17058 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.64 % Allowed : 17.96 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.20), residues: 1660 helix: -0.33 (0.19), residues: 681 sheet: -0.53 (0.31), residues: 260 loop : -0.64 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP X 113 HIS 0.015 0.002 HIS U 56 PHE 0.034 0.002 PHE F 80 TYR 0.021 0.002 TYR L 117 ARG 0.013 0.001 ARG Y 212 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 402 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 TYR cc_start: 0.7274 (t80) cc_final: 0.7066 (t80) REVERT: D 51 TYR cc_start: 0.9405 (t80) cc_final: 0.8981 (t80) REVERT: D 71 GLN cc_start: 0.9110 (mt0) cc_final: 0.8818 (mt0) REVERT: D 72 PHE cc_start: 0.9693 (t80) cc_final: 0.9483 (t80) REVERT: D 74 ASN cc_start: 0.9179 (m-40) cc_final: 0.8544 (m-40) REVERT: D 75 TYR cc_start: 0.9272 (m-80) cc_final: 0.9015 (m-80) REVERT: D 76 TYR cc_start: 0.9569 (t80) cc_final: 0.9254 (t80) REVERT: D 77 LYS cc_start: 0.9604 (mtmt) cc_final: 0.9285 (mtmm) REVERT: D 182 PHE cc_start: 0.9300 (t80) cc_final: 0.9012 (t80) REVERT: D 196 ASN cc_start: 0.8836 (m-40) cc_final: 0.8389 (m110) REVERT: E 16 ILE cc_start: 0.9643 (tp) cc_final: 0.9376 (mp) REVERT: E 30 ILE cc_start: 0.8102 (mm) cc_final: 0.7814 (mm) REVERT: E 37 THR cc_start: 0.9574 (OUTLIER) cc_final: 0.9060 (t) REVERT: E 54 ARG cc_start: 0.9101 (mmm160) cc_final: 0.8765 (mpt180) REVERT: E 60 ILE cc_start: 0.9614 (tt) cc_final: 0.9016 (pt) REVERT: E 64 MET cc_start: 0.9573 (mmt) cc_final: 0.9188 (mmt) REVERT: E 65 GLU cc_start: 0.9449 (tp30) cc_final: 0.9126 (tp30) REVERT: E 66 LYS cc_start: 0.8828 (mmtt) cc_final: 0.8530 (mmmt) REVERT: E 95 PHE cc_start: 0.9213 (t80) cc_final: 0.8831 (t80) REVERT: E 128 TYR cc_start: 0.8980 (m-80) cc_final: 0.8764 (m-80) REVERT: F 65 GLU cc_start: 0.8857 (pt0) cc_final: 0.8568 (tt0) REVERT: F 88 MET cc_start: 0.8912 (ttm) cc_final: 0.8699 (ttm) REVERT: F 90 MET cc_start: 0.8617 (mmm) cc_final: 0.8200 (mmm) REVERT: F 91 ARG cc_start: 0.8935 (ttt180) cc_final: 0.8728 (ttt180) REVERT: F 92 THR cc_start: 0.9061 (p) cc_final: 0.8723 (p) REVERT: H 38 ASN cc_start: 0.9386 (t0) cc_final: 0.8864 (t0) REVERT: H 85 ILE cc_start: 0.9527 (mm) cc_final: 0.9101 (mp) REVERT: H 86 TYR cc_start: 0.8416 (m-80) cc_final: 0.7441 (m-10) REVERT: H 90 ASP cc_start: 0.9614 (p0) cc_final: 0.9276 (p0) REVERT: H 124 GLU cc_start: 0.9153 (tt0) cc_final: 0.8493 (tt0) REVERT: H 128 TYR cc_start: 0.9062 (m-10) cc_final: 0.8671 (m-80) REVERT: K 125 LYS cc_start: 0.9412 (pttt) cc_final: 0.9083 (ptpt) REVERT: L 5 ASN cc_start: 0.9311 (t0) cc_final: 0.8727 (t0) REVERT: L 73 ASN cc_start: 0.8510 (p0) cc_final: 0.8276 (p0) REVERT: L 90 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8506 (mm) REVERT: L 103 ASP cc_start: 0.9160 (t0) cc_final: 0.8831 (t0) REVERT: L 117 TYR cc_start: 0.8246 (m-80) cc_final: 0.8019 (m-10) REVERT: O 62 GLN cc_start: 0.9365 (tp40) cc_final: 0.9043 (tp40) REVERT: O 65 LYS cc_start: 0.9380 (mttm) cc_final: 0.8936 (mtmm) REVERT: O 68 ASP cc_start: 0.9299 (m-30) cc_final: 0.9048 (m-30) REVERT: O 73 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8503 (mmmt) REVERT: P 12 LYS cc_start: 0.9003 (mttp) cc_final: 0.8782 (mttp) REVERT: P 26 ASN cc_start: 0.8999 (m110) cc_final: 0.8644 (m110) REVERT: P 31 ARG cc_start: 0.8938 (ttp80) cc_final: 0.8506 (ttp-110) REVERT: Q 9 GLN cc_start: 0.8611 (pt0) cc_final: 0.8339 (pp30) REVERT: Q 17 MET cc_start: 0.8981 (mtm) cc_final: 0.8496 (mtm) REVERT: Q 38 ILE cc_start: 0.9762 (pt) cc_final: 0.9436 (mm) REVERT: Q 49 GLU cc_start: 0.8668 (pm20) cc_final: 0.8301 (pm20) REVERT: Q 52 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8811 (tm-30) REVERT: Q 63 GLU cc_start: 0.8465 (pm20) cc_final: 0.8242 (pm20) REVERT: R 52 GLN cc_start: 0.9512 (tp40) cc_final: 0.9184 (tt0) REVERT: R 73 ARG cc_start: 0.8882 (ttm110) cc_final: 0.8190 (mtm-85) REVERT: T 13 GLN cc_start: 0.9523 (pt0) cc_final: 0.9025 (pp30) REVERT: U 19 PHE cc_start: 0.8266 (t80) cc_final: 0.7983 (t80) REVERT: U 23 CYS cc_start: 0.8559 (p) cc_final: 0.8242 (p) REVERT: U 36 GLU cc_start: 0.9687 (tp30) cc_final: 0.9240 (tp30) REVERT: U 40 LYS cc_start: 0.9451 (ttpt) cc_final: 0.9072 (tttp) REVERT: U 42 THR cc_start: 0.9095 (t) cc_final: 0.8821 (m) REVERT: U 56 HIS cc_start: 0.9589 (t-90) cc_final: 0.9336 (m90) REVERT: X 21 PHE cc_start: 0.8854 (m-80) cc_final: 0.8539 (m-80) REVERT: X 40 ILE cc_start: 0.9469 (OUTLIER) cc_final: 0.9098 (mp) REVERT: X 62 LEU cc_start: 0.9168 (mt) cc_final: 0.8298 (pp) REVERT: X 101 LEU cc_start: 0.9321 (mp) cc_final: 0.8989 (tp) REVERT: Y 24 PHE cc_start: 0.8611 (m-80) cc_final: 0.8032 (m-80) REVERT: Y 41 MET cc_start: 0.8707 (mmm) cc_final: 0.8300 (mmm) REVERT: Y 116 TYR cc_start: 0.8051 (m-80) cc_final: 0.7408 (m-10) REVERT: Y 155 LYS cc_start: 0.8540 (tppp) cc_final: 0.8238 (tppt) REVERT: Y 157 TYR cc_start: 0.8646 (t80) cc_final: 0.8220 (t80) REVERT: Y 163 MET cc_start: 0.9637 (mmm) cc_final: 0.9203 (mmm) REVERT: Y 202 HIS cc_start: 0.9214 (m90) cc_final: 0.8938 (m90) REVERT: Y 241 MET cc_start: 0.9371 (mmm) cc_final: 0.8766 (mmt) REVERT: Y 247 MET cc_start: 0.8965 (mtm) cc_final: 0.8711 (mpp) REVERT: Y 257 TYR cc_start: 0.9480 (m-80) cc_final: 0.9222 (m-80) outliers start: 37 outliers final: 14 residues processed: 418 average time/residue: 0.5691 time to fit residues: 361.1512 Evaluate side-chains 359 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 342 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 51 SER Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 200 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 196 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 236 optimal weight: 20.0000 chunk 255 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 234 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 189 optimal weight: 0.2980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 54 GLN D 89 ASN ** F 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36819 Z= 0.196 Angle : 0.645 13.050 54562 Z= 0.342 Chirality : 0.037 0.322 6890 Planarity : 0.005 0.108 3327 Dihedral : 23.766 179.027 17053 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.42 % Allowed : 20.53 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.20), residues: 1660 helix: -0.12 (0.19), residues: 678 sheet: -0.66 (0.29), residues: 306 loop : -0.49 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 42 HIS 0.007 0.001 HIS X 56 PHE 0.017 0.002 PHE K 105 TYR 0.032 0.002 TYR R 70 ARG 0.011 0.001 ARG D 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 366 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 TYR cc_start: 0.7192 (t80) cc_final: 0.6904 (t80) REVERT: D 51 TYR cc_start: 0.9347 (t80) cc_final: 0.8749 (t80) REVERT: D 71 GLN cc_start: 0.9141 (mt0) cc_final: 0.8669 (mt0) REVERT: D 75 TYR cc_start: 0.9267 (m-80) cc_final: 0.8739 (m-80) REVERT: D 76 TYR cc_start: 0.9570 (t80) cc_final: 0.9300 (t80) REVERT: D 77 LYS cc_start: 0.9607 (mtmt) cc_final: 0.9341 (mtmt) REVERT: D 182 PHE cc_start: 0.9242 (t80) cc_final: 0.8906 (t80) REVERT: D 196 ASN cc_start: 0.8865 (m-40) cc_final: 0.8480 (m110) REVERT: E 16 ILE cc_start: 0.9658 (tp) cc_final: 0.9351 (mp) REVERT: E 30 ILE cc_start: 0.8337 (mm) cc_final: 0.8037 (mm) REVERT: E 37 THR cc_start: 0.9543 (m) cc_final: 0.9275 (t) REVERT: E 54 ARG cc_start: 0.9046 (mmm160) cc_final: 0.8800 (mpt180) REVERT: E 64 MET cc_start: 0.9635 (mmt) cc_final: 0.9393 (mmm) REVERT: E 65 GLU cc_start: 0.9424 (tp30) cc_final: 0.8861 (tp30) REVERT: E 66 LYS cc_start: 0.8852 (mmtt) cc_final: 0.8464 (mmmt) REVERT: E 95 PHE cc_start: 0.9247 (t80) cc_final: 0.8856 (t80) REVERT: E 126 LYS cc_start: 0.9194 (tptp) cc_final: 0.8793 (tppt) REVERT: F 9 MET cc_start: 0.9154 (pmm) cc_final: 0.8846 (pmm) REVERT: F 24 ARG cc_start: 0.9069 (ptp-110) cc_final: 0.8656 (ptp-170) REVERT: F 88 MET cc_start: 0.9038 (ttm) cc_final: 0.8708 (ttm) REVERT: F 90 MET cc_start: 0.8548 (mmm) cc_final: 0.8214 (mmm) REVERT: H 38 ASN cc_start: 0.9419 (t0) cc_final: 0.8942 (t0) REVERT: H 85 ILE cc_start: 0.9518 (mm) cc_final: 0.9170 (mp) REVERT: H 86 TYR cc_start: 0.8393 (m-80) cc_final: 0.7444 (m-10) REVERT: H 124 GLU cc_start: 0.9300 (tt0) cc_final: 0.8453 (tt0) REVERT: H 127 CYS cc_start: 0.9639 (p) cc_final: 0.9373 (p) REVERT: K 125 LYS cc_start: 0.9518 (pttt) cc_final: 0.9174 (ptpt) REVERT: L 5 ASN cc_start: 0.9342 (t0) cc_final: 0.8764 (t0) REVERT: L 73 ASN cc_start: 0.8799 (p0) cc_final: 0.8503 (p0) REVERT: L 90 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8535 (mm) REVERT: L 103 ASP cc_start: 0.9182 (t0) cc_final: 0.8933 (t0) REVERT: O 62 GLN cc_start: 0.9428 (tp40) cc_final: 0.8828 (tp40) REVERT: O 65 LYS cc_start: 0.9449 (mttm) cc_final: 0.8893 (mtmm) REVERT: O 68 ASP cc_start: 0.9257 (m-30) cc_final: 0.9030 (m-30) REVERT: P 26 ASN cc_start: 0.9003 (m110) cc_final: 0.8651 (m110) REVERT: Q 38 ILE cc_start: 0.9729 (pt) cc_final: 0.9482 (mm) REVERT: Q 39 LYS cc_start: 0.9750 (mmmt) cc_final: 0.9503 (mmmt) REVERT: R 73 ARG cc_start: 0.8862 (ttm110) cc_final: 0.8423 (tpm170) REVERT: T 13 GLN cc_start: 0.9511 (pt0) cc_final: 0.9152 (pp30) REVERT: T 29 ARG cc_start: 0.9248 (OUTLIER) cc_final: 0.8919 (ptp90) REVERT: U 19 PHE cc_start: 0.8397 (t80) cc_final: 0.8139 (t80) REVERT: U 23 CYS cc_start: 0.8748 (p) cc_final: 0.8425 (p) REVERT: U 35 ARG cc_start: 0.9217 (ttm170) cc_final: 0.8735 (mmt90) REVERT: U 36 GLU cc_start: 0.9731 (tp30) cc_final: 0.9301 (tp30) REVERT: U 40 LYS cc_start: 0.9352 (ttpt) cc_final: 0.8852 (tttm) REVERT: U 56 HIS cc_start: 0.9611 (t-90) cc_final: 0.9361 (m90) REVERT: X 62 LEU cc_start: 0.9187 (mt) cc_final: 0.8371 (pp) REVERT: X 145 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8257 (t0) REVERT: Y 24 PHE cc_start: 0.8663 (m-80) cc_final: 0.8057 (m-80) REVERT: Y 123 MET cc_start: 0.9739 (mpp) cc_final: 0.9455 (pmm) REVERT: Y 155 LYS cc_start: 0.8608 (tppp) cc_final: 0.8000 (tppt) REVERT: Y 163 MET cc_start: 0.9642 (mmm) cc_final: 0.9201 (mmm) REVERT: Y 241 MET cc_start: 0.9356 (mmm) cc_final: 0.8938 (mmm) REVERT: Y 247 MET cc_start: 0.9062 (mtm) cc_final: 0.8828 (mpp) outliers start: 48 outliers final: 22 residues processed: 392 average time/residue: 0.5487 time to fit residues: 328.9424 Evaluate side-chains 350 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 325 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 29 ARG Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain X residue 149 HIS Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 110 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 30.0000 chunk 177 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 112 optimal weight: 0.5980 chunk 158 optimal weight: 20.0000 chunk 237 optimal weight: 20.0000 chunk 251 optimal weight: 30.0000 chunk 124 optimal weight: 9.9990 chunk 224 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 overall best weight: 4.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 HIS ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN X 109 ASN X 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 36819 Z= 0.272 Angle : 0.664 14.622 54562 Z= 0.349 Chirality : 0.037 0.304 6890 Planarity : 0.005 0.109 3327 Dihedral : 23.872 177.842 17053 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 23.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.28 % Allowed : 21.45 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.20), residues: 1660 helix: -0.11 (0.19), residues: 687 sheet: -0.83 (0.29), residues: 321 loop : -0.43 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 42 HIS 0.007 0.001 HIS X 56 PHE 0.012 0.002 PHE Q 28 TYR 0.025 0.002 TYR H 128 ARG 0.008 0.001 ARG Q 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 338 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 TYR cc_start: 0.7190 (t80) cc_final: 0.6881 (t80) REVERT: D 51 TYR cc_start: 0.9324 (t80) cc_final: 0.9002 (t80) REVERT: D 75 TYR cc_start: 0.9214 (m-80) cc_final: 0.8819 (m-80) REVERT: D 76 TYR cc_start: 0.9587 (t80) cc_final: 0.9302 (t80) REVERT: D 77 LYS cc_start: 0.9605 (mtmt) cc_final: 0.9371 (mtmm) REVERT: D 182 PHE cc_start: 0.9185 (t80) cc_final: 0.8818 (t80) REVERT: D 196 ASN cc_start: 0.8921 (m-40) cc_final: 0.8488 (m110) REVERT: E 14 LYS cc_start: 0.9574 (tppp) cc_final: 0.9360 (ttmm) REVERT: E 16 ILE cc_start: 0.9616 (tp) cc_final: 0.9317 (mp) REVERT: E 30 ILE cc_start: 0.8350 (mm) cc_final: 0.8000 (mm) REVERT: E 37 THR cc_start: 0.9464 (m) cc_final: 0.9222 (t) REVERT: E 60 ILE cc_start: 0.9637 (tt) cc_final: 0.9128 (pt) REVERT: E 65 GLU cc_start: 0.9416 (tp30) cc_final: 0.8983 (tp30) REVERT: E 66 LYS cc_start: 0.8844 (mmtt) cc_final: 0.8492 (mmmt) REVERT: E 68 ARG cc_start: 0.8720 (ptp-110) cc_final: 0.8336 (ptp-170) REVERT: E 95 PHE cc_start: 0.9215 (t80) cc_final: 0.8910 (t80) REVERT: E 126 LYS cc_start: 0.9342 (tptp) cc_final: 0.8785 (tppt) REVERT: E 141 ILE cc_start: 0.9777 (mm) cc_final: 0.9458 (tp) REVERT: E 145 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8408 (mm-30) REVERT: F 24 ARG cc_start: 0.9139 (ptp-110) cc_final: 0.8846 (ptp-170) REVERT: F 88 MET cc_start: 0.8843 (ttm) cc_final: 0.8531 (ttm) REVERT: F 90 MET cc_start: 0.8383 (mmm) cc_final: 0.8084 (mmm) REVERT: H 38 ASN cc_start: 0.9439 (t0) cc_final: 0.9014 (t0) REVERT: H 85 ILE cc_start: 0.9471 (mm) cc_final: 0.9201 (mm) REVERT: H 86 TYR cc_start: 0.8523 (m-80) cc_final: 0.7469 (m-80) REVERT: H 91 GLU cc_start: 0.8978 (pm20) cc_final: 0.8754 (pm20) REVERT: H 96 MET cc_start: 0.8959 (mtp) cc_final: 0.8737 (mtp) REVERT: H 124 GLU cc_start: 0.9330 (tt0) cc_final: 0.8418 (tt0) REVERT: H 128 TYR cc_start: 0.9058 (m-80) cc_final: 0.8689 (m-80) REVERT: K 13 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7596 (tpm170) REVERT: K 125 LYS cc_start: 0.9555 (pttt) cc_final: 0.9241 (ptpt) REVERT: L 5 ASN cc_start: 0.9350 (t0) cc_final: 0.8868 (t0) REVERT: L 7 LEU cc_start: 0.9897 (mm) cc_final: 0.9653 (mp) REVERT: L 66 TYR cc_start: 0.8943 (t80) cc_final: 0.8739 (t80) REVERT: O 62 GLN cc_start: 0.9443 (tp40) cc_final: 0.9236 (tp40) REVERT: O 68 ASP cc_start: 0.9252 (m-30) cc_final: 0.9039 (m-30) REVERT: P 26 ASN cc_start: 0.9015 (m110) cc_final: 0.8731 (m110) REVERT: P 52 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8950 (pp) REVERT: Q 39 LYS cc_start: 0.9736 (mmmt) cc_final: 0.9386 (mmmt) REVERT: T 13 GLN cc_start: 0.9486 (pt0) cc_final: 0.9067 (pp30) REVERT: T 29 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.8885 (ptp90) REVERT: U 19 PHE cc_start: 0.8480 (t80) cc_final: 0.8154 (t80) REVERT: U 23 CYS cc_start: 0.8891 (p) cc_final: 0.8538 (p) REVERT: U 35 ARG cc_start: 0.9230 (ttm170) cc_final: 0.8730 (mmt90) REVERT: U 36 GLU cc_start: 0.9732 (tp30) cc_final: 0.9283 (tp30) REVERT: U 40 LYS cc_start: 0.9284 (ttpt) cc_final: 0.8743 (mtpt) REVERT: X 62 LEU cc_start: 0.9179 (mt) cc_final: 0.8343 (pp) REVERT: X 145 ASN cc_start: 0.8798 (OUTLIER) cc_final: 0.8302 (t0) REVERT: Y 155 LYS cc_start: 0.8625 (tppp) cc_final: 0.8038 (tppt) REVERT: Y 163 MET cc_start: 0.9613 (mmm) cc_final: 0.9158 (mmm) REVERT: Y 241 MET cc_start: 0.9354 (mmm) cc_final: 0.8917 (mmm) REVERT: Y 247 MET cc_start: 0.9194 (mtm) cc_final: 0.8717 (mtp) outliers start: 60 outliers final: 34 residues processed: 374 average time/residue: 0.5306 time to fit residues: 305.3515 Evaluate side-chains 344 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 306 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 13 ARG Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 29 ARG Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 142 GLN Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain X residue 149 HIS Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 202 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 5.9990 chunk 142 optimal weight: 0.0370 chunk 3 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 chunk 103 optimal weight: 6.9990 chunk 214 optimal weight: 3.9990 chunk 173 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 225 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 overall best weight: 4.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN E 148 ASN K 15 GLN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 113 ASN Y 197 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 36819 Z= 0.271 Angle : 0.651 13.615 54562 Z= 0.342 Chirality : 0.036 0.305 6890 Planarity : 0.005 0.108 3327 Dihedral : 23.949 178.922 17053 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 23.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.85 % Allowed : 22.17 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.20), residues: 1660 helix: -0.05 (0.19), residues: 683 sheet: -0.84 (0.29), residues: 318 loop : -0.53 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP X 113 HIS 0.006 0.001 HIS X 56 PHE 0.013 0.001 PHE K 105 TYR 0.015 0.002 TYR R 23 ARG 0.011 0.001 ARG Q 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 336 time to evaluate : 2.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 TYR cc_start: 0.7124 (t80) cc_final: 0.6847 (t80) REVERT: D 51 TYR cc_start: 0.9286 (t80) cc_final: 0.8909 (t80) REVERT: D 74 ASN cc_start: 0.9231 (m-40) cc_final: 0.8874 (m-40) REVERT: D 75 TYR cc_start: 0.9230 (m-80) cc_final: 0.8791 (m-80) REVERT: D 76 TYR cc_start: 0.9595 (t80) cc_final: 0.9367 (t80) REVERT: D 182 PHE cc_start: 0.9141 (t80) cc_final: 0.8767 (t80) REVERT: D 196 ASN cc_start: 0.8992 (m-40) cc_final: 0.8569 (m110) REVERT: E 14 LYS cc_start: 0.9595 (tppp) cc_final: 0.9393 (ttmm) REVERT: E 16 ILE cc_start: 0.9605 (tp) cc_final: 0.9338 (mp) REVERT: E 60 ILE cc_start: 0.9431 (OUTLIER) cc_final: 0.9178 (pt) REVERT: E 65 GLU cc_start: 0.9410 (tp30) cc_final: 0.8886 (tp30) REVERT: E 66 LYS cc_start: 0.8821 (mmtt) cc_final: 0.8408 (mmmt) REVERT: E 69 ARG cc_start: 0.9549 (ttm-80) cc_final: 0.9297 (ttm-80) REVERT: E 70 ASN cc_start: 0.9345 (OUTLIER) cc_final: 0.9115 (p0) REVERT: E 126 LYS cc_start: 0.9309 (tptp) cc_final: 0.8802 (tppt) REVERT: F 52 ASN cc_start: 0.8926 (t0) cc_final: 0.8711 (t0) REVERT: F 88 MET cc_start: 0.9023 (ttm) cc_final: 0.8693 (ttm) REVERT: F 90 MET cc_start: 0.8289 (mmm) cc_final: 0.7806 (mmm) REVERT: H 38 ASN cc_start: 0.9414 (t0) cc_final: 0.9042 (t0) REVERT: H 80 ARG cc_start: 0.8718 (mtp-110) cc_final: 0.8452 (mtp-110) REVERT: H 85 ILE cc_start: 0.9450 (mm) cc_final: 0.9162 (mm) REVERT: H 86 TYR cc_start: 0.8673 (m-80) cc_final: 0.7555 (m-80) REVERT: H 124 GLU cc_start: 0.9339 (tt0) cc_final: 0.8461 (tt0) REVERT: K 125 LYS cc_start: 0.9553 (pttt) cc_final: 0.9181 (ptpt) REVERT: L 5 ASN cc_start: 0.9330 (t0) cc_final: 0.8758 (t0) REVERT: O 62 GLN cc_start: 0.9450 (tp40) cc_final: 0.9234 (tp40) REVERT: O 68 ASP cc_start: 0.9262 (m-30) cc_final: 0.9048 (m-30) REVERT: P 26 ASN cc_start: 0.9045 (m110) cc_final: 0.8750 (m110) REVERT: P 52 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8908 (pp) REVERT: Q 39 LYS cc_start: 0.9722 (mmmt) cc_final: 0.9391 (mmmt) REVERT: T 13 GLN cc_start: 0.9491 (pt0) cc_final: 0.9064 (pp30) REVERT: U 23 CYS cc_start: 0.8890 (p) cc_final: 0.8649 (p) REVERT: U 35 ARG cc_start: 0.9216 (ttm170) cc_final: 0.8748 (mmt90) REVERT: U 36 GLU cc_start: 0.9747 (tp30) cc_final: 0.9293 (tp30) REVERT: U 55 ARG cc_start: 0.9584 (mtm-85) cc_final: 0.9342 (mtm110) REVERT: X 62 LEU cc_start: 0.9224 (mt) cc_final: 0.8432 (pp) REVERT: Y 116 TYR cc_start: 0.7943 (m-80) cc_final: 0.6922 (m-80) REVERT: Y 123 MET cc_start: 0.9748 (mpp) cc_final: 0.9509 (pmm) REVERT: Y 163 MET cc_start: 0.9601 (mmm) cc_final: 0.9151 (mmm) REVERT: Y 241 MET cc_start: 0.9337 (mmm) cc_final: 0.8879 (mmm) REVERT: Y 247 MET cc_start: 0.9228 (mtm) cc_final: 0.8772 (mtp) outliers start: 68 outliers final: 50 residues processed: 378 average time/residue: 0.5558 time to fit residues: 321.8201 Evaluate side-chains 363 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 310 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain K residue 127 ARG Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 29 ARG Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 46 LYS Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain X residue 149 HIS Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 57 GLU Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 202 HIS Chi-restraints excluded: chain Y residue 206 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 9.9990 chunk 226 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 147 optimal weight: 0.0020 chunk 62 optimal weight: 10.0000 chunk 251 optimal weight: 0.5980 chunk 208 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 overall best weight: 4.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 74 HIS T 70 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 36819 Z= 0.255 Angle : 0.639 13.629 54562 Z= 0.336 Chirality : 0.036 0.304 6890 Planarity : 0.005 0.109 3327 Dihedral : 23.965 178.060 17053 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 24.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.56 % Allowed : 23.95 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.20), residues: 1660 helix: -0.04 (0.19), residues: 678 sheet: -0.88 (0.29), residues: 320 loop : -0.49 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP X 113 HIS 0.007 0.001 HIS X 56 PHE 0.016 0.002 PHE X 136 TYR 0.025 0.002 TYR R 64 ARG 0.013 0.001 ARG Q 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 327 time to evaluate : 2.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 TYR cc_start: 0.7212 (t80) cc_final: 0.6903 (t80) REVERT: D 51 TYR cc_start: 0.9288 (t80) cc_final: 0.8948 (t80) REVERT: D 75 TYR cc_start: 0.9264 (m-80) cc_final: 0.8718 (m-80) REVERT: D 76 TYR cc_start: 0.9603 (t80) cc_final: 0.9285 (t80) REVERT: D 77 LYS cc_start: 0.9415 (mtmt) cc_final: 0.9205 (mtmt) REVERT: D 182 PHE cc_start: 0.9126 (t80) cc_final: 0.8755 (t80) REVERT: D 196 ASN cc_start: 0.9007 (m-40) cc_final: 0.8606 (m110) REVERT: E 13 GLU cc_start: 0.9132 (pp20) cc_final: 0.8849 (tm-30) REVERT: E 14 LYS cc_start: 0.9612 (tppp) cc_final: 0.9406 (tppp) REVERT: E 16 ILE cc_start: 0.9577 (tp) cc_final: 0.9295 (mp) REVERT: E 22 SER cc_start: 0.8930 (t) cc_final: 0.8653 (p) REVERT: E 64 MET cc_start: 0.9616 (mmp) cc_final: 0.9310 (mmp) REVERT: E 65 GLU cc_start: 0.9430 (tp30) cc_final: 0.8819 (tp30) REVERT: E 66 LYS cc_start: 0.8686 (mmtt) cc_final: 0.8277 (mmmt) REVERT: E 71 MET cc_start: 0.8712 (ttt) cc_final: 0.8320 (tmt) REVERT: E 126 LYS cc_start: 0.9270 (tptp) cc_final: 0.8774 (tppt) REVERT: F 9 MET cc_start: 0.8974 (pmm) cc_final: 0.8619 (pmm) REVERT: F 88 MET cc_start: 0.9079 (ttm) cc_final: 0.8376 (tpp) REVERT: F 90 MET cc_start: 0.7673 (mmm) cc_final: 0.7182 (mmm) REVERT: F 91 ARG cc_start: 0.8871 (ttt180) cc_final: 0.8262 (ttt180) REVERT: H 38 ASN cc_start: 0.9378 (t0) cc_final: 0.9061 (t0) REVERT: H 71 VAL cc_start: 0.9201 (OUTLIER) cc_final: 0.8739 (m) REVERT: H 80 ARG cc_start: 0.8712 (mtp-110) cc_final: 0.8442 (mtp-110) REVERT: H 86 TYR cc_start: 0.8694 (m-80) cc_final: 0.8362 (m-80) REVERT: K 13 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7897 (tpm170) REVERT: K 125 LYS cc_start: 0.9518 (pttt) cc_final: 0.9147 (ptpt) REVERT: L 5 ASN cc_start: 0.9342 (t0) cc_final: 0.8784 (t0) REVERT: L 7 LEU cc_start: 0.9889 (mm) cc_final: 0.9605 (mp) REVERT: O 68 ASP cc_start: 0.9227 (m-30) cc_final: 0.9017 (m-30) REVERT: P 26 ASN cc_start: 0.9048 (m110) cc_final: 0.8754 (m110) REVERT: P 52 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8965 (pp) REVERT: Q 39 LYS cc_start: 0.9754 (mmmt) cc_final: 0.9477 (mmmt) REVERT: R 20 GLU cc_start: 0.8064 (tp30) cc_final: 0.7066 (tm-30) REVERT: T 13 GLN cc_start: 0.9489 (pt0) cc_final: 0.9065 (pp30) REVERT: U 35 ARG cc_start: 0.9218 (ttm170) cc_final: 0.8765 (mmt90) REVERT: U 36 GLU cc_start: 0.9772 (tp30) cc_final: 0.9353 (tp30) REVERT: U 56 HIS cc_start: 0.9630 (t-90) cc_final: 0.9304 (m90) REVERT: X 62 LEU cc_start: 0.9167 (mt) cc_final: 0.8388 (pp) REVERT: X 105 MET cc_start: 0.7066 (ptt) cc_final: 0.6532 (pmm) REVERT: X 110 ARG cc_start: 0.8922 (ttp-170) cc_final: 0.8366 (tpp-160) REVERT: Y 163 MET cc_start: 0.9586 (mmm) cc_final: 0.9147 (mmm) REVERT: Y 241 MET cc_start: 0.9363 (mmm) cc_final: 0.8888 (mmm) REVERT: Y 247 MET cc_start: 0.9242 (mtm) cc_final: 0.8793 (mtp) outliers start: 64 outliers final: 47 residues processed: 368 average time/residue: 0.5397 time to fit residues: 306.1518 Evaluate side-chains 361 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 311 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain K residue 13 ARG Chi-restraints excluded: chain K residue 80 LYS Chi-restraints excluded: chain K residue 127 ARG Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 29 ARG Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 44 GLU Chi-restraints excluded: chain U residue 46 LYS Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain X residue 149 HIS Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 57 GLU Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 206 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 211 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 250 optimal weight: 10.0000 chunk 156 optimal weight: 20.0000 chunk 152 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 36819 Z= 0.283 Angle : 0.661 13.984 54562 Z= 0.346 Chirality : 0.036 0.301 6890 Planarity : 0.005 0.109 3327 Dihedral : 24.004 179.509 17053 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 26.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.78 % Allowed : 25.02 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.20), residues: 1660 helix: -0.05 (0.19), residues: 678 sheet: -0.99 (0.29), residues: 326 loop : -0.47 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP X 113 HIS 0.007 0.001 HIS X 56 PHE 0.024 0.002 PHE H 66 TYR 0.019 0.002 TYR Q 34 ARG 0.006 0.001 ARG Q 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 315 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 TYR cc_start: 0.7228 (t80) cc_final: 0.6924 (t80) REVERT: D 51 TYR cc_start: 0.9278 (t80) cc_final: 0.8997 (t80) REVERT: D 75 TYR cc_start: 0.9305 (m-80) cc_final: 0.8922 (m-80) REVERT: D 76 TYR cc_start: 0.9609 (t80) cc_final: 0.9328 (t80) REVERT: D 182 PHE cc_start: 0.9130 (t80) cc_final: 0.8740 (t80) REVERT: D 196 ASN cc_start: 0.9065 (m-40) cc_final: 0.8682 (m110) REVERT: E 13 GLU cc_start: 0.9070 (pp20) cc_final: 0.8804 (tm-30) REVERT: E 14 LYS cc_start: 0.9626 (tppp) cc_final: 0.9412 (tppp) REVERT: E 16 ILE cc_start: 0.9562 (tp) cc_final: 0.9279 (mp) REVERT: E 22 SER cc_start: 0.8907 (t) cc_final: 0.8668 (p) REVERT: E 64 MET cc_start: 0.9634 (mmp) cc_final: 0.9325 (mmp) REVERT: E 65 GLU cc_start: 0.9404 (tp30) cc_final: 0.9108 (tm-30) REVERT: E 70 ASN cc_start: 0.9373 (OUTLIER) cc_final: 0.9173 (p0) REVERT: E 126 LYS cc_start: 0.9271 (tptp) cc_final: 0.8830 (tppt) REVERT: F 88 MET cc_start: 0.9039 (ttm) cc_final: 0.8606 (ttt) REVERT: F 91 ARG cc_start: 0.8848 (ttt180) cc_final: 0.8235 (ttt180) REVERT: H 38 ASN cc_start: 0.9386 (t0) cc_final: 0.9122 (t0) REVERT: H 80 ARG cc_start: 0.8777 (mtp-110) cc_final: 0.8422 (mtp-110) REVERT: H 86 TYR cc_start: 0.8661 (m-80) cc_final: 0.8407 (m-80) REVERT: H 96 MET cc_start: 0.8963 (mtp) cc_final: 0.8729 (mtp) REVERT: K 13 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.8013 (tpm170) REVERT: K 125 LYS cc_start: 0.9524 (pttt) cc_final: 0.9148 (ptpt) REVERT: L 5 ASN cc_start: 0.9335 (t0) cc_final: 0.8667 (t0) REVERT: O 68 ASP cc_start: 0.9267 (m-30) cc_final: 0.9064 (m-30) REVERT: P 1 MET cc_start: 0.8581 (pmm) cc_final: 0.8159 (pmm) REVERT: P 26 ASN cc_start: 0.9090 (m110) cc_final: 0.8810 (m110) REVERT: P 52 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8753 (pp) REVERT: Q 39 LYS cc_start: 0.9749 (mmmt) cc_final: 0.9468 (mmmt) REVERT: T 13 GLN cc_start: 0.9505 (pt0) cc_final: 0.9070 (pp30) REVERT: U 35 ARG cc_start: 0.9215 (ttm170) cc_final: 0.8781 (mmt90) REVERT: U 36 GLU cc_start: 0.9774 (tp30) cc_final: 0.9358 (tp30) REVERT: U 56 HIS cc_start: 0.9627 (t-90) cc_final: 0.9312 (m-70) REVERT: X 62 LEU cc_start: 0.9111 (mt) cc_final: 0.8361 (pp) REVERT: X 105 MET cc_start: 0.6997 (ptt) cc_final: 0.6426 (pmm) REVERT: X 124 MET cc_start: 0.8975 (mmm) cc_final: 0.8709 (tpp) REVERT: Y 116 TYR cc_start: 0.7647 (m-80) cc_final: 0.6536 (m-80) REVERT: Y 123 MET cc_start: 0.9748 (mpp) cc_final: 0.9533 (pmm) REVERT: Y 163 MET cc_start: 0.9567 (mmm) cc_final: 0.9114 (mmm) REVERT: Y 241 MET cc_start: 0.9362 (mmm) cc_final: 0.8889 (mmm) REVERT: Y 247 MET cc_start: 0.9260 (mtm) cc_final: 0.8802 (mtp) outliers start: 67 outliers final: 54 residues processed: 361 average time/residue: 0.5295 time to fit residues: 295.9510 Evaluate side-chains 359 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 302 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 13 ARG Chi-restraints excluded: chain K residue 127 ARG Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 29 ARG Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 44 GLU Chi-restraints excluded: chain U residue 46 LYS Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain X residue 149 HIS Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 57 GLU Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 206 ASP Chi-restraints excluded: chain Y residue 231 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 149 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 123 optimal weight: 0.0980 chunk 23 optimal weight: 10.0000 chunk 196 optimal weight: 8.9990 overall best weight: 5.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 164 GLN F 3 HIS ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 ASN ** X 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 36819 Z= 0.322 Angle : 0.691 13.671 54562 Z= 0.360 Chirality : 0.037 0.299 6890 Planarity : 0.005 0.109 3327 Dihedral : 24.072 179.231 17053 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 29.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 5.42 % Allowed : 25.37 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.20), residues: 1660 helix: -0.19 (0.19), residues: 679 sheet: -1.03 (0.29), residues: 325 loop : -0.59 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP X 113 HIS 0.021 0.002 HIS F 94 PHE 0.021 0.002 PHE R 10 TYR 0.034 0.002 TYR R 23 ARG 0.008 0.001 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 309 time to evaluate : 2.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 TYR cc_start: 0.7276 (t80) cc_final: 0.6970 (t80) REVERT: D 51 TYR cc_start: 0.9277 (t80) cc_final: 0.9013 (t80) REVERT: D 75 TYR cc_start: 0.9335 (m-80) cc_final: 0.8932 (m-80) REVERT: D 76 TYR cc_start: 0.9624 (t80) cc_final: 0.9345 (t80) REVERT: D 78 GLU cc_start: 0.9296 (OUTLIER) cc_final: 0.9010 (tp30) REVERT: D 182 PHE cc_start: 0.9122 (t80) cc_final: 0.8694 (t80) REVERT: D 196 ASN cc_start: 0.9105 (m-40) cc_final: 0.8726 (m110) REVERT: E 13 GLU cc_start: 0.9049 (pp20) cc_final: 0.8817 (tm-30) REVERT: E 14 LYS cc_start: 0.9619 (tppp) cc_final: 0.9337 (tppp) REVERT: E 16 ILE cc_start: 0.9567 (tp) cc_final: 0.9292 (mp) REVERT: E 64 MET cc_start: 0.9649 (mmp) cc_final: 0.9355 (mmp) REVERT: E 65 GLU cc_start: 0.9395 (tp30) cc_final: 0.9135 (tm-30) REVERT: E 126 LYS cc_start: 0.9301 (tptp) cc_final: 0.8832 (tppt) REVERT: F 1 MET cc_start: 0.9554 (ttm) cc_final: 0.9248 (ttp) REVERT: F 91 ARG cc_start: 0.8747 (ttt180) cc_final: 0.8177 (ttt180) REVERT: H 38 ASN cc_start: 0.9399 (t0) cc_final: 0.9165 (t0) REVERT: H 71 VAL cc_start: 0.9224 (OUTLIER) cc_final: 0.8981 (p) REVERT: H 80 ARG cc_start: 0.8856 (mtp-110) cc_final: 0.8526 (mtp-110) REVERT: H 86 TYR cc_start: 0.8624 (m-80) cc_final: 0.8324 (m-80) REVERT: H 96 MET cc_start: 0.9000 (mtp) cc_final: 0.8752 (mtp) REVERT: K 13 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7203 (tpm170) REVERT: K 42 LEU cc_start: 0.9307 (mm) cc_final: 0.8709 (tp) REVERT: K 77 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.8190 (t80) REVERT: K 125 LYS cc_start: 0.9496 (pttt) cc_final: 0.9122 (ptpt) REVERT: L 5 ASN cc_start: 0.9335 (t0) cc_final: 0.8768 (t0) REVERT: L 7 LEU cc_start: 0.9876 (mm) cc_final: 0.9630 (mp) REVERT: O 68 ASP cc_start: 0.9277 (m-30) cc_final: 0.9077 (m-30) REVERT: P 26 ASN cc_start: 0.9099 (m110) cc_final: 0.8823 (m110) REVERT: Q 39 LYS cc_start: 0.9710 (mmmt) cc_final: 0.9364 (mmmt) REVERT: T 13 GLN cc_start: 0.9527 (pt0) cc_final: 0.9089 (pp30) REVERT: U 35 ARG cc_start: 0.9206 (ttm170) cc_final: 0.8802 (mmt90) REVERT: U 36 GLU cc_start: 0.9765 (tp30) cc_final: 0.9299 (tp30) REVERT: U 56 HIS cc_start: 0.9625 (t-90) cc_final: 0.9289 (m-70) REVERT: X 62 LEU cc_start: 0.9094 (mt) cc_final: 0.8331 (pp) REVERT: X 124 MET cc_start: 0.8993 (mmm) cc_final: 0.8707 (mmm) REVERT: Y 116 TYR cc_start: 0.7635 (m-80) cc_final: 0.6523 (m-80) REVERT: Y 163 MET cc_start: 0.9567 (mmm) cc_final: 0.9069 (mmm) REVERT: Y 241 MET cc_start: 0.9364 (mmm) cc_final: 0.8888 (mmm) REVERT: Y 247 MET cc_start: 0.9268 (mtm) cc_final: 0.8803 (mtp) outliers start: 76 outliers final: 60 residues processed: 360 average time/residue: 0.5519 time to fit residues: 308.0594 Evaluate side-chains 365 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 301 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 13 ARG Chi-restraints excluded: chain K residue 77 TYR Chi-restraints excluded: chain K residue 127 ARG Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 29 ARG Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 44 GLU Chi-restraints excluded: chain U residue 46 LYS Chi-restraints excluded: chain U residue 49 LYS Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 141 ILE Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain X residue 149 HIS Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 57 GLU Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 206 ASP Chi-restraints excluded: chain Y residue 231 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 5.9990 chunk 240 optimal weight: 0.6980 chunk 219 optimal weight: 5.9990 chunk 233 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 211 optimal weight: 0.6980 chunk 220 optimal weight: 0.9980 chunk 232 optimal weight: 9.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 ASN K 15 GLN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN X 73 ASN ** X 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36819 Z= 0.185 Angle : 0.640 13.674 54562 Z= 0.331 Chirality : 0.034 0.309 6890 Planarity : 0.005 0.110 3327 Dihedral : 23.997 177.226 17053 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.92 % Allowed : 26.94 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.20), residues: 1660 helix: 0.04 (0.19), residues: 672 sheet: -0.92 (0.29), residues: 313 loop : -0.50 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP X 113 HIS 0.010 0.001 HIS F 94 PHE 0.022 0.002 PHE R 10 TYR 0.017 0.002 TYR Y 263 ARG 0.006 0.001 ARG Q 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 335 time to evaluate : 2.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 51 TYR cc_start: 0.9232 (t80) cc_final: 0.8939 (t80) REVERT: D 75 TYR cc_start: 0.9321 (m-80) cc_final: 0.8650 (m-80) REVERT: D 76 TYR cc_start: 0.9580 (t80) cc_final: 0.9331 (t80) REVERT: D 77 LYS cc_start: 0.9385 (mtmt) cc_final: 0.9054 (mtmm) REVERT: D 78 GLU cc_start: 0.9290 (OUTLIER) cc_final: 0.8949 (tp30) REVERT: D 182 PHE cc_start: 0.9164 (t80) cc_final: 0.8717 (t80) REVERT: D 196 ASN cc_start: 0.9037 (m-40) cc_final: 0.8736 (m-40) REVERT: E 13 GLU cc_start: 0.9071 (pp20) cc_final: 0.8828 (tm-30) REVERT: E 16 ILE cc_start: 0.9541 (tp) cc_final: 0.9282 (mp) REVERT: E 64 MET cc_start: 0.9623 (mmp) cc_final: 0.9354 (mmp) REVERT: E 65 GLU cc_start: 0.9431 (tp30) cc_final: 0.9042 (tm-30) REVERT: E 66 LYS cc_start: 0.8962 (mmtt) cc_final: 0.8277 (mmtt) REVERT: E 71 MET cc_start: 0.8690 (ttt) cc_final: 0.8365 (ttt) REVERT: E 126 LYS cc_start: 0.9194 (tptp) cc_final: 0.8779 (tppt) REVERT: E 147 MET cc_start: 0.8688 (tpt) cc_final: 0.8469 (tpt) REVERT: F 1 MET cc_start: 0.9412 (ttm) cc_final: 0.9133 (tmm) REVERT: F 52 ASN cc_start: 0.9126 (t0) cc_final: 0.8741 (p0) REVERT: H 38 ASN cc_start: 0.9343 (t0) cc_final: 0.9139 (t0) REVERT: H 71 VAL cc_start: 0.9223 (OUTLIER) cc_final: 0.8805 (m) REVERT: H 80 ARG cc_start: 0.8854 (mtp-110) cc_final: 0.8465 (mtp-110) REVERT: H 86 TYR cc_start: 0.8600 (m-80) cc_final: 0.8322 (m-80) REVERT: H 127 CYS cc_start: 0.9465 (p) cc_final: 0.9165 (t) REVERT: H 128 TYR cc_start: 0.9012 (m-80) cc_final: 0.8524 (m-80) REVERT: K 42 LEU cc_start: 0.9195 (mm) cc_final: 0.8609 (tp) REVERT: K 77 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.7942 (t80) REVERT: L 5 ASN cc_start: 0.9363 (t0) cc_final: 0.8893 (t0) REVERT: L 7 LEU cc_start: 0.9867 (mm) cc_final: 0.9598 (mp) REVERT: O 65 LYS cc_start: 0.9491 (ptpp) cc_final: 0.9201 (ptpp) REVERT: O 68 ASP cc_start: 0.9270 (m-30) cc_final: 0.9064 (m-30) REVERT: P 1 MET cc_start: 0.8635 (pmm) cc_final: 0.8263 (pmm) REVERT: P 12 LYS cc_start: 0.8802 (ttpp) cc_final: 0.8283 (tmtt) REVERT: P 26 ASN cc_start: 0.9134 (m110) cc_final: 0.8845 (m110) REVERT: Q 36 LYS cc_start: 0.9094 (tttm) cc_final: 0.8841 (tttt) REVERT: Q 39 LYS cc_start: 0.9724 (mmmt) cc_final: 0.9486 (mmmt) REVERT: R 64 TYR cc_start: 0.9105 (t80) cc_final: 0.8778 (t80) REVERT: T 13 GLN cc_start: 0.9466 (pt0) cc_final: 0.9048 (pp30) REVERT: U 35 ARG cc_start: 0.9207 (ttm170) cc_final: 0.8848 (mmt90) REVERT: U 36 GLU cc_start: 0.9753 (tp30) cc_final: 0.9304 (tp30) REVERT: X 62 LEU cc_start: 0.9123 (mt) cc_final: 0.8334 (pp) REVERT: X 105 MET cc_start: 0.6842 (ptt) cc_final: 0.6615 (pmm) REVERT: Y 57 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.9002 (pt0) REVERT: Y 123 MET cc_start: 0.9748 (mpp) cc_final: 0.9541 (pmm) REVERT: Y 155 LYS cc_start: 0.8909 (tptt) cc_final: 0.8704 (tptt) REVERT: Y 163 MET cc_start: 0.9553 (mmm) cc_final: 0.9094 (mmm) REVERT: Y 241 MET cc_start: 0.9331 (mmm) cc_final: 0.8547 (mmt) REVERT: Y 247 MET cc_start: 0.9236 (mtm) cc_final: 0.8829 (mtp) REVERT: Y 263 TYR cc_start: 0.9563 (t80) cc_final: 0.9361 (t80) outliers start: 55 outliers final: 42 residues processed: 369 average time/residue: 0.5552 time to fit residues: 319.2498 Evaluate side-chains 362 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 316 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 77 TYR Chi-restraints excluded: chain K residue 127 ARG Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 29 ARG Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 46 LYS Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain X residue 149 HIS Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 57 GLU Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 206 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 4.9990 chunk 246 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 259 optimal weight: 0.8980 chunk 238 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 126 optimal weight: 0.0670 overall best weight: 1.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 GLN Q 50 ASN ** X 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 36819 Z= 0.165 Angle : 0.656 25.371 54562 Z= 0.336 Chirality : 0.034 0.295 6890 Planarity : 0.005 0.111 3327 Dihedral : 23.841 177.863 17053 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.14 % Allowed : 27.80 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.20), residues: 1660 helix: 0.11 (0.19), residues: 671 sheet: -0.96 (0.29), residues: 313 loop : -0.53 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP Q 73 HIS 0.009 0.001 HIS X 56 PHE 0.022 0.002 PHE R 10 TYR 0.044 0.002 TYR R 23 ARG 0.006 0.001 ARG Q 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 332 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 51 TYR cc_start: 0.9216 (t80) cc_final: 0.8921 (t80) REVERT: D 75 TYR cc_start: 0.9348 (m-80) cc_final: 0.8701 (m-80) REVERT: D 76 TYR cc_start: 0.9572 (t80) cc_final: 0.9297 (t80) REVERT: D 77 LYS cc_start: 0.9401 (mtmt) cc_final: 0.9037 (mtmm) REVERT: D 182 PHE cc_start: 0.9153 (t80) cc_final: 0.8703 (t80) REVERT: D 196 ASN cc_start: 0.8994 (m-40) cc_final: 0.8679 (m-40) REVERT: E 14 LYS cc_start: 0.9544 (tppp) cc_final: 0.9266 (tptp) REVERT: E 16 ILE cc_start: 0.9520 (tp) cc_final: 0.9279 (mp) REVERT: E 64 MET cc_start: 0.9595 (mmp) cc_final: 0.9355 (mmp) REVERT: E 65 GLU cc_start: 0.9420 (tp30) cc_final: 0.9006 (tm-30) REVERT: E 66 LYS cc_start: 0.8970 (mmtt) cc_final: 0.8152 (mmtt) REVERT: E 126 LYS cc_start: 0.9141 (tptp) cc_final: 0.8773 (tppt) REVERT: F 1 MET cc_start: 0.9431 (ttm) cc_final: 0.9133 (tmm) REVERT: F 9 MET cc_start: 0.9037 (pmm) cc_final: 0.8542 (pmm) REVERT: F 88 MET cc_start: 0.8358 (tpp) cc_final: 0.7886 (tmm) REVERT: F 91 ARG cc_start: 0.8893 (tpp80) cc_final: 0.8474 (ttt180) REVERT: H 71 VAL cc_start: 0.9146 (OUTLIER) cc_final: 0.8759 (m) REVERT: H 86 TYR cc_start: 0.8572 (m-80) cc_final: 0.8293 (m-10) REVERT: H 127 CYS cc_start: 0.9413 (p) cc_final: 0.9145 (t) REVERT: H 128 TYR cc_start: 0.8999 (m-80) cc_final: 0.8530 (m-80) REVERT: K 42 LEU cc_start: 0.9169 (mm) cc_final: 0.8516 (tp) REVERT: K 125 LYS cc_start: 0.9420 (pttt) cc_final: 0.9186 (ptmt) REVERT: L 5 ASN cc_start: 0.9368 (t0) cc_final: 0.8869 (t0) REVERT: O 59 MET cc_start: 0.9270 (mmp) cc_final: 0.9001 (mmm) REVERT: O 68 ASP cc_start: 0.9244 (m-30) cc_final: 0.9026 (m-30) REVERT: P 1 MET cc_start: 0.8571 (pmm) cc_final: 0.8269 (pmm) REVERT: P 26 ASN cc_start: 0.9124 (m110) cc_final: 0.8842 (m110) REVERT: Q 38 ILE cc_start: 0.9678 (mp) cc_final: 0.9411 (tt) REVERT: T 13 GLN cc_start: 0.9388 (pt0) cc_final: 0.8994 (pp30) REVERT: U 35 ARG cc_start: 0.9222 (ttm170) cc_final: 0.8875 (mmt90) REVERT: U 36 GLU cc_start: 0.9757 (tp30) cc_final: 0.9358 (tp30) REVERT: U 37 PHE cc_start: 0.9061 (m-80) cc_final: 0.8434 (m-10) REVERT: U 56 HIS cc_start: 0.9599 (t-90) cc_final: 0.9233 (m-70) REVERT: X 62 LEU cc_start: 0.9080 (mt) cc_final: 0.8276 (pp) REVERT: X 105 MET cc_start: 0.6612 (ptt) cc_final: 0.6132 (pmm) REVERT: X 124 MET cc_start: 0.8973 (mmm) cc_final: 0.8432 (tpp) REVERT: Y 116 TYR cc_start: 0.7723 (m-80) cc_final: 0.6687 (m-80) REVERT: Y 123 MET cc_start: 0.9744 (mpp) cc_final: 0.9536 (pmm) REVERT: Y 155 LYS cc_start: 0.8946 (tptt) cc_final: 0.8649 (tppt) REVERT: Y 163 MET cc_start: 0.9550 (mmm) cc_final: 0.9104 (mmm) REVERT: Y 241 MET cc_start: 0.9312 (mmm) cc_final: 0.8789 (mmm) REVERT: Y 247 MET cc_start: 0.9243 (mtm) cc_final: 0.8856 (mtp) outliers start: 44 outliers final: 39 residues processed: 356 average time/residue: 0.5466 time to fit residues: 301.4779 Evaluate side-chains 356 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 316 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 127 ARG Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 43 LYS Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 29 ARG Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 145 ASN Chi-restraints excluded: chain X residue 149 HIS Chi-restraints excluded: chain Y residue 42 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 206 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 30.0000 chunk 219 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 206 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 212 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 overall best weight: 4.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.025067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2451 r_free = 0.2451 target = 0.020010 restraints weight = 448482.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.020803 restraints weight = 178328.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.021300 restraints weight = 102890.842| |-----------------------------------------------------------------------------| r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 36819 Z= 0.292 Angle : 0.688 18.087 54562 Z= 0.358 Chirality : 0.036 0.293 6890 Planarity : 0.005 0.111 3327 Dihedral : 23.926 177.603 17053 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 28.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.63 % Rotamer: Outliers : 3.49 % Allowed : 27.87 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.20), residues: 1660 helix: -0.08 (0.19), residues: 667 sheet: -1.08 (0.29), residues: 313 loop : -0.51 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 170 HIS 0.008 0.001 HIS X 56 PHE 0.019 0.002 PHE R 10 TYR 0.036 0.002 TYR R 64 ARG 0.012 0.001 ARG U 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6512.98 seconds wall clock time: 121 minutes 8.06 seconds (7268.06 seconds total)