Starting phenix.real_space_refine on Sun Mar 24 14:37:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqb_0482/03_2024/6nqb_0482.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqb_0482/03_2024/6nqb_0482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqb_0482/03_2024/6nqb_0482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqb_0482/03_2024/6nqb_0482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqb_0482/03_2024/6nqb_0482.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqb_0482/03_2024/6nqb_0482.pdb" } resolution = 3.8 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= 1.000 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 1341 5.49 5 Mg 1 5.21 5 S 49 5.16 5 C 21496 2.51 5 N 7902 2.21 5 O 11781 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J ARG 45": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "D ARG 2": "NH1" <-> "NH2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 187": "NH1" <-> "NH2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "P PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 52": "NH1" <-> "NH2" Residue "B PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 42570 Number of models: 1 Model: "" Number of chains: 17 Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 91} Chain: "N" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "S" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 594 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "A" Number of atoms: 28767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 28767 Classifications: {'RNA': 1341} Modifications used: {'rna2p_pur': 98, 'rna2p_pyr': 68, 'rna3p_pur': 663, 'rna3p_pyr': 512} Link IDs: {'rna2p': 165, 'rna3p': 1175} Chain breaks: 2 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: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1089 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 143} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 630 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain breaks: 1 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: "L" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "O" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 698 Classifications: {'peptide': 86} Link IDs: {'TRANS': 85} Chain: "P" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 629 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "Q" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 641 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 405 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain breaks: 1 Chain: "T" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 659 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1696 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.02, per 1000 atoms: 0.49 Number of scatterers: 42570 At special positions: 0 Unit cell: (204.943, 215.673, 154.512, 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 49 16.00 P 1341 15.00 Mg 1 11.99 O 11781 8.00 N 7902 7.00 C 21496 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: 23.89 Conformation dependent library (CDL) restraints added in 2.6 seconds 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3256 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 18 sheets defined 33.4% alpha, 9.4% beta 250 base pairs and 620 stacking pairs defined. Time for finding SS restraints: 17.89 Creating SS restraints... Processing helix chain 'C' and resid 27 through 40 removed outlier: 4.580A pdb=" N LEU C 32 " --> pdb=" O PHE C 28 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG C 39 " --> pdb=" O ASP C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 removed outlier: 3.889A pdb=" N VAL C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 93 removed outlier: 3.760A pdb=" N VAL C 89 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASP C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.796A pdb=" N ILE C 119 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 143 removed outlier: 4.367A pdb=" N LYS C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN C 138 " --> pdb=" O LYS C 134 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 21 Processing helix chain 'J' and resid 22 through 27 removed outlier: 4.352A pdb=" N GLU J 27 " --> pdb=" O ALA J 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 18 removed outlier: 4.596A pdb=" N VAL N 10 " --> pdb=" O LYS N 6 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS N 11 " --> pdb=" O ALA N 7 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU N 15 " --> pdb=" O LYS N 11 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ALA N 16 " --> pdb=" O ARG N 12 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP N 17 " --> pdb=" O VAL N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 28 removed outlier: 3.536A pdb=" N LYS N 27 " --> pdb=" O ALA N 24 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA N 28 " --> pdb=" O GLU N 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 24 through 28' Processing helix chain 'N' and resid 41 through 49 removed outlier: 3.918A pdb=" N LEU N 45 " --> pdb=" O TRP N 41 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR N 49 " --> pdb=" O LEU N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 89 removed outlier: 3.867A pdb=" N ARG N 84 " --> pdb=" O ARG N 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 16 Processing helix chain 'S' and resid 40 through 44 removed outlier: 3.851A pdb=" N ILE S 44 " --> pdb=" O PRO S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 73 removed outlier: 4.139A pdb=" N GLU S 72 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE S 73 " --> pdb=" O LEU S 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 69 through 73' Processing helix chain 'D' and resid 8 through 14 Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.564A pdb=" N ILE D 27 " --> pdb=" O VAL D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 61 removed outlier: 4.056A pdb=" N VAL D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN D 53 " --> pdb=" O ASP D 49 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU D 56 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 81 removed outlier: 3.738A pdb=" N ASN D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 79 " --> pdb=" O TYR D 75 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG D 80 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 95 Processing helix chain 'D' and resid 96 through 104 removed outlier: 3.573A pdb=" N ARG D 103 " --> pdb=" O ASN D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 119 Processing helix chain 'D' and resid 146 through 149 Processing helix chain 'D' and resid 157 through 164 removed outlier: 3.619A pdb=" N ALA D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 204 removed outlier: 3.609A pdb=" N VAL D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU D 202 " --> pdb=" O LEU D 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 67 removed outlier: 4.051A pdb=" N ILE E 59 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU E 64 " --> pdb=" O GLN E 60 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA E 66 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 removed outlier: 4.159A pdb=" N ALA E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 145 removed outlier: 3.990A pdb=" N VAL E 136 " --> pdb=" O PRO E 132 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG E 137 " --> pdb=" O ILE E 133 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA E 138 " --> pdb=" O ASN E 134 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR E 139 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 157 removed outlier: 3.835A pdb=" N LYS E 155 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 16 No H-bonds generated for 'chain 'F' and resid 14 through 16' Processing helix chain 'F' and resid 17 through 25 removed outlier: 3.588A pdb=" N MET F 21 " --> pdb=" O GLN F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 71 through 76 removed outlier: 3.694A pdb=" N GLU F 75 " --> pdb=" O ILE F 71 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR F 76 " --> pdb=" O ASP F 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 71 through 76' Processing helix chain 'H' and resid 6 through 15 removed outlier: 3.745A pdb=" N ARG H 12 " --> pdb=" O ASP H 8 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG H 14 " --> pdb=" O LEU H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 40 removed outlier: 3.783A pdb=" N ALA H 34 " --> pdb=" O LYS H 30 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA H 36 " --> pdb=" O LYS H 32 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL H 38 " --> pdb=" O ALA H 34 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU H 39 " --> pdb=" O ILE H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 112 through 116 removed outlier: 4.409A pdb=" N ALA H 115 " --> pdb=" O ASP H 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 7 removed outlier: 3.596A pdb=" N LEU L 6 " --> pdb=" O THR L 2 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 9 removed outlier: 3.642A pdb=" N LYS O 9 " --> pdb=" O GLU O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 42 removed outlier: 3.525A pdb=" N ALA O 33 " --> pdb=" O ALA O 29 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU O 38 " --> pdb=" O GLN O 34 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS O 41 " --> pdb=" O HIS O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 73 removed outlier: 3.587A pdb=" N MET O 58 " --> pdb=" O GLY O 54 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU O 66 " --> pdb=" O ARG O 62 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR O 68 " --> pdb=" O LYS O 64 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS O 72 " --> pdb=" O TYR O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 85 Processing helix chain 'P' and resid 53 through 64 removed outlier: 4.107A pdb=" N ILE P 57 " --> pdb=" O ASP P 53 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY P 62 " --> pdb=" O ALA P 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY P 64 " --> pdb=" O TRP P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 78 removed outlier: 4.322A pdb=" N LYS P 76 " --> pdb=" O ALA P 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 30 removed outlier: 3.557A pdb=" N LEU R 28 " --> pdb=" O ASP R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 Processing helix chain 'R' and resid 51 through 60 removed outlier: 3.958A pdb=" N ARG R 56 " --> pdb=" O ARG R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 64 removed outlier: 3.596A pdb=" N LEU R 64 " --> pdb=" O ALA R 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 61 through 64' Processing helix chain 'T' and resid 6 through 41 removed outlier: 3.889A pdb=" N GLN T 12 " --> pdb=" O LYS T 8 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN T 20 " --> pdb=" O ALA T 16 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG T 23 " --> pdb=" O HIS T 19 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER T 25 " --> pdb=" O ALA T 21 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET T 26 " --> pdb=" O SER T 22 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE T 30 " --> pdb=" O MET T 26 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL T 34 " --> pdb=" O PHE T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 60 removed outlier: 3.619A pdb=" N PHE T 50 " --> pdb=" O ALA T 46 " (cutoff:3.500A) Proline residue: T 55 - end of helix removed outlier: 3.725A pdb=" N ASP T 58 " --> pdb=" O GLN T 54 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN T 60 " --> pdb=" O ILE T 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 86 removed outlier: 3.904A pdb=" N THR T 79 " --> pdb=" O LYS T 75 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS T 84 " --> pdb=" O ALA T 80 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA T 86 " --> pdb=" O ILE T 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 61 removed outlier: 4.320A pdb=" N ASN B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 59 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 117 through 122 Processing helix chain 'B' and resid 131 through 136 removed outlier: 4.290A pdb=" N MET B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 131 through 136' Processing helix chain 'B' and resid 136 through 147 removed outlier: 3.827A pdb=" N LEU B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLU B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASN B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 151 removed outlier: 4.019A pdb=" N LYS B 151 " --> pdb=" O GLY B 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 148 through 151' Processing helix chain 'B' and resid 168 through 176 Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 205 through 217 removed outlier: 3.592A pdb=" N VAL B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 213 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 51 through 55 removed outlier: 3.511A pdb=" N ARG C 53 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS C 68 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL C 65 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA C 103 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE C 67 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 168 through 169 Processing sheet with id=AA3, first strand: chain 'J' and resid 6 through 12 removed outlier: 3.707A pdb=" N LEU J 10 " --> pdb=" O ARG J 72 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N THR J 69 " --> pdb=" O ARG J 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 65 through 66 removed outlier: 3.747A pdb=" N LYS N 96 " --> pdb=" O GLU J 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 50 through 51 Processing sheet with id=AA6, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AA7, first strand: chain 'D' and resid 170 through 172 Processing sheet with id=AA8, first strand: chain 'E' and resid 12 through 14 removed outlier: 3.967A pdb=" N THR E 36 " --> pdb=" O GLY E 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 85 through 87 removed outlier: 3.748A pdb=" N LEU E 123 " --> pdb=" O GLN E 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 5 through 8 Processing sheet with id=AB2, first strand: chain 'H' and resid 23 through 24 removed outlier: 3.988A pdb=" N ASP H 47 " --> pdb=" O THR H 61 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 100 through 104 removed outlier: 7.386A pdb=" N ILE H 100 " --> pdb=" O TYR H 127 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N TYR H 127 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL H 102 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU H 123 " --> pdb=" O SER H 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.597A pdb=" N GLY L 31 " --> pdb=" O ILE L 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 51 through 55 Processing sheet with id=AB6, first strand: chain 'P' and resid 18 through 21 removed outlier: 4.345A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG P 51 " --> pdb=" O PHE P 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Q' and resid 7 through 10 removed outlier: 4.025A pdb=" N ARG Q 76 " --> pdb=" O GLU Q 59 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ARG Q 61 " --> pdb=" O LEU Q 74 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU Q 74 " --> pdb=" O ARG Q 61 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N LYS Q 70 " --> pdb=" O LYS Q 42 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N HIS Q 44 " --> pdb=" O LYS Q 70 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TRP Q 72 " --> pdb=" O HIS Q 44 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR Q 41 " --> pdb=" O ILE Q 24 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE Q 24 " --> pdb=" O THR Q 41 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 30 through 33 removed outlier: 4.303A pdb=" N GLY B 32 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 89 through 91 removed outlier: 6.165A pdb=" N PHE B 68 " --> pdb=" O VAL B 91 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 903 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 594 hydrogen bonds 890 hydrogen bond angles 0 basepair planarities 250 basepair parallelities 620 stacking parallelities Total time for adding SS restraints: 27.92 Time building geometry restraints manager: 25.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5140 1.32 - 1.45: 19614 1.45 - 1.57: 18690 1.57 - 1.69: 2681 1.69 - 1.81: 88 Bond restraints: 46213 Sorted by residual: bond pdb=" C VAL B 46 " pdb=" N PRO B 47 " ideal model delta sigma weight residual 1.335 1.383 -0.047 1.30e-02 5.92e+03 1.33e+01 bond pdb=" CA ARG R 62 " pdb=" C ARG R 62 " ideal model delta sigma weight residual 1.522 1.569 -0.046 1.37e-02 5.33e+03 1.14e+01 bond pdb=" CA THR B 71 " pdb=" C THR B 71 " ideal model delta sigma weight residual 1.518 1.629 -0.111 4.01e-02 6.22e+02 7.62e+00 bond pdb=" C SER H 78 " pdb=" N ARG H 79 " ideal model delta sigma weight residual 1.339 1.202 0.137 5.57e-02 3.22e+02 6.09e+00 bond pdb=" CA TYR C 167 " pdb=" CB TYR C 167 " ideal model delta sigma weight residual 1.524 1.492 0.032 1.62e-02 3.81e+03 3.89e+00 ... (remaining 46208 not shown) Histogram of bond angle deviations from ideal: 97.74 - 105.35: 6716 105.35 - 112.96: 27245 112.96 - 120.57: 20184 120.57 - 128.18: 12725 128.18 - 135.79: 2182 Bond angle restraints: 69052 Sorted by residual: angle pdb=" C THR B 19 " pdb=" N ARG B 20 " pdb=" CA ARG B 20 " ideal model delta sigma weight residual 120.38 130.91 -10.53 1.37e+00 5.33e-01 5.90e+01 angle pdb=" N ARG Q 5 " pdb=" CA ARG Q 5 " pdb=" C ARG Q 5 " ideal model delta sigma weight residual 114.64 105.31 9.33 1.52e+00 4.33e-01 3.77e+01 angle pdb=" N ALA F 66 " pdb=" CA ALA F 66 " pdb=" C ALA F 66 " ideal model delta sigma weight residual 109.60 116.39 -6.79 1.15e+00 7.56e-01 3.48e+01 angle pdb=" N THR F 26 " pdb=" CA THR F 26 " pdb=" C THR F 26 " ideal model delta sigma weight residual 113.38 106.31 7.07 1.23e+00 6.61e-01 3.30e+01 angle pdb=" N ILE H 6 " pdb=" CA ILE H 6 " pdb=" C ILE H 6 " ideal model delta sigma weight residual 112.96 107.35 5.61 1.00e+00 1.00e+00 3.15e+01 ... (remaining 69047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 25844 35.95 - 71.91: 3342 71.91 - 107.86: 419 107.86 - 143.82: 9 143.82 - 179.77: 11 Dihedral angle restraints: 29625 sinusoidal: 24596 harmonic: 5029 Sorted by residual: 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 65.79 134.21 1 1.50e+01 4.44e-03 7.24e+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 52.23 179.77 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C A1322 " pdb=" C1' C A1322 " pdb=" N1 C A1322 " pdb=" C2 C A1322 " ideal model delta sinusoidal sigma weight residual -128.00 48.56 -176.56 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 29622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 7983 0.075 - 0.151: 765 0.151 - 0.226: 58 0.226 - 0.301: 9 0.301 - 0.377: 9 Chirality restraints: 8824 Sorted by residual: chirality pdb=" C1' U A 365 " pdb=" O4' U A 365 " pdb=" C2' U A 365 " pdb=" N1 U A 365 " both_signs ideal model delta sigma weight residual False 2.47 2.09 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CB ILE Q 54 " pdb=" CA ILE Q 54 " pdb=" CG1 ILE Q 54 " pdb=" CG2 ILE Q 54 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C3' C A 372 " pdb=" C4' C A 372 " pdb=" O3' C A 372 " pdb=" C2' C A 372 " both_signs ideal model delta sigma weight residual False -2.74 -2.39 -0.35 2.00e-01 2.50e+01 3.07e+00 ... (remaining 8821 not shown) Planarity restraints: 3762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 23 " 0.053 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO B 24 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 24 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 24 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS L 26 " 0.046 5.00e-02 4.00e+02 6.98e-02 7.78e+00 pdb=" N PRO L 27 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO L 27 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO L 27 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN P 40 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO P 41 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO P 41 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO P 41 " -0.038 5.00e-02 4.00e+02 ... (remaining 3759 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 7047 2.75 - 3.29: 37901 3.29 - 3.83: 89123 3.83 - 4.36: 101178 4.36 - 4.90: 137572 Nonbonded interactions: 372821 Sorted by model distance: nonbonded pdb=" O2' U A 662 " pdb=" OP1 G A 836 " model vdw 2.216 2.440 nonbonded pdb=" O SER N 99 " pdb=" O2' C A1114 " model vdw 2.227 2.440 nonbonded pdb=" O2' U A 343 " pdb=" O6 G A 346 " model vdw 2.239 2.440 nonbonded pdb=" OP2 C A 522 " pdb=" OH TYR L 65 " model vdw 2.260 2.440 nonbonded pdb=" OP1 U A 62 " pdb=" O2' C A 385 " model vdw 2.263 2.440 ... (remaining 372816 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: 1.220 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: 0.030 Extract box with map and model: 7.890 Check model and map are aligned: 0.810 Set scattering table: 0.450 Process input model: 130.420 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.130 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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 : 0.006 0.137 46213 Z= 0.340 Angle : 0.981 18.166 69052 Z= 0.501 Chirality : 0.047 0.377 8824 Planarity : 0.006 0.080 3762 Dihedral : 24.158 179.773 26369 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.64 % Favored : 86.31 % Rotamer: Outliers : 0.41 % Allowed : 5.01 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -5.36 (0.15), residues: 1716 helix: -4.19 (0.12), residues: 487 sheet: -3.39 (0.28), residues: 231 loop : -3.37 (0.16), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP B 22 HIS 0.020 0.002 HIS J 15 PHE 0.028 0.003 PHE B 49 TYR 0.029 0.003 TYR L 65 ARG 0.018 0.001 ARG D 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 542 time to evaluate : 2.536 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: C 32 LEU cc_start: 0.8512 (pt) cc_final: 0.8054 (tp) REVERT: C 36 PHE cc_start: 0.9092 (t80) cc_final: 0.8796 (t80) REVERT: C 42 LEU cc_start: 0.8055 (mt) cc_final: 0.7803 (mt) REVERT: C 108 PRO cc_start: 0.6733 (Cg_endo) cc_final: 0.6220 (Cg_exo) REVERT: C 182 ASP cc_start: 0.7466 (t0) cc_final: 0.6990 (t0) REVERT: C 186 SER cc_start: 0.8401 (t) cc_final: 0.8033 (t) REVERT: J 13 PHE cc_start: 0.7941 (m-10) cc_final: 0.7732 (m-10) REVERT: J 52 LEU cc_start: 0.9090 (mp) cc_final: 0.8602 (tp) REVERT: J 69 THR cc_start: 0.7293 (m) cc_final: 0.6947 (p) REVERT: J 88 MET cc_start: 0.6361 (mpp) cc_final: 0.6075 (ptp) REVERT: N 57 SER cc_start: 0.7049 (m) cc_final: 0.6165 (t) REVERT: N 82 LYS cc_start: 0.8129 (mmpt) cc_final: 0.7755 (mmtm) REVERT: N 83 VAL cc_start: 0.9056 (t) cc_final: 0.8852 (t) REVERT: N 92 ILE cc_start: 0.8438 (mt) cc_final: 0.8113 (pt) REVERT: D 69 ARG cc_start: 0.8708 (mmp-170) cc_final: 0.7763 (ptt180) REVERT: D 147 LYS cc_start: 0.7851 (mttt) cc_final: 0.7563 (mmmt) REVERT: D 195 ASN cc_start: 0.8263 (m-40) cc_final: 0.7839 (t0) REVERT: E 93 VAL cc_start: 0.9586 (t) cc_final: 0.9367 (m) REVERT: E 94 PHE cc_start: 0.8663 (t80) cc_final: 0.8252 (t80) REVERT: F 4 TYR cc_start: 0.5743 (m-80) cc_final: 0.4908 (m-80) REVERT: F 17 GLN cc_start: 0.8004 (tt0) cc_final: 0.7798 (tp40) REVERT: F 68 GLN cc_start: 0.6458 (pm20) cc_final: 0.4737 (mm-40) REVERT: F 89 VAL cc_start: 0.7443 (t) cc_final: 0.6487 (m) REVERT: H 30 LYS cc_start: 0.8473 (mmpt) cc_final: 0.7802 (mttt) REVERT: H 37 ASN cc_start: 0.8116 (t0) cc_final: 0.7108 (t0) REVERT: H 87 ARG cc_start: 0.7385 (ttm170) cc_final: 0.7020 (ttt-90) REVERT: L 63 THR cc_start: 0.6556 (t) cc_final: 0.6124 (t) REVERT: L 69 GLU cc_start: 0.7089 (tt0) cc_final: 0.6315 (mm-30) REVERT: O 16 ARG cc_start: 0.8055 (ptp-170) cc_final: 0.7348 (mtm-85) REVERT: O 38 LEU cc_start: 0.8516 (mt) cc_final: 0.8087 (tt) REVERT: P 5 ARG cc_start: 0.8456 (pmt100) cc_final: 0.8254 (ptt90) REVERT: P 35 ARG cc_start: 0.8844 (tmm160) cc_final: 0.8638 (tmm-80) REVERT: Q 59 GLU cc_start: 0.7849 (mm-30) cc_final: 0.6304 (mm-30) REVERT: T 31 ILE cc_start: 0.9434 (mt) cc_final: 0.9110 (mt) REVERT: T 53 MET cc_start: 0.8431 (ptm) cc_final: 0.8074 (ppp) REVERT: T 56 ILE cc_start: 0.8880 (mt) cc_final: 0.8506 (mm) REVERT: B 29 PHE cc_start: 0.8392 (m-80) cc_final: 0.8012 (m-80) REVERT: B 112 ARG cc_start: 0.4519 (ttt90) cc_final: 0.1826 (ttm110) REVERT: B 136 ARG cc_start: 0.6514 (mtp180) cc_final: 0.6003 (mtm110) REVERT: B 191 ASP cc_start: 0.6505 (t0) cc_final: 0.6287 (t70) outliers start: 6 outliers final: 1 residues processed: 545 average time/residue: 0.6597 time to fit residues: 548.2083 Evaluate side-chains 318 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 317 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 11 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 252 optimal weight: 0.9990 chunk 226 optimal weight: 0.0000 chunk 125 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 152 optimal weight: 40.0000 chunk 121 optimal weight: 10.0000 chunk 234 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 142 optimal weight: 40.0000 chunk 174 optimal weight: 30.0000 chunk 271 optimal weight: 0.1980 overall best weight: 2.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 5 HIS C 24 ASN C 175 HIS ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 GLN D 99 ASN D 119 HIS ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 HIS F 63 ASN H 15 ASN H 17 GLN H 75 GLN L 72 ASN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 73 HIS T 20 ASN ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 74 HIS B 121 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 46213 Z= 0.191 Angle : 0.684 15.152 69052 Z= 0.355 Chirality : 0.039 0.272 8824 Planarity : 0.006 0.068 3762 Dihedral : 24.978 179.312 22895 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.42 % Favored : 88.46 % Rotamer: Outliers : 3.85 % Allowed : 15.11 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -4.39 (0.17), residues: 1716 helix: -2.79 (0.18), residues: 516 sheet: -3.09 (0.30), residues: 225 loop : -3.02 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Q 72 HIS 0.009 0.001 HIS R 73 PHE 0.024 0.002 PHE D 106 TYR 0.015 0.002 TYR H 64 ARG 0.016 0.001 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 393 time to evaluate : 2.419 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: C 36 PHE cc_start: 0.9042 (t80) cc_final: 0.8678 (t80) REVERT: C 111 ASP cc_start: 0.8180 (t70) cc_final: 0.7909 (t70) REVERT: C 141 MET cc_start: 0.8770 (mmm) cc_final: 0.7418 (mmm) REVERT: C 143 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6248 (mp) REVERT: C 182 ASP cc_start: 0.7506 (t0) cc_final: 0.7073 (t0) REVERT: J 52 LEU cc_start: 0.9074 (mp) cc_final: 0.8457 (tp) REVERT: J 85 ASP cc_start: 0.7686 (m-30) cc_final: 0.7006 (m-30) REVERT: J 88 MET cc_start: 0.6242 (mpp) cc_final: 0.5804 (ptp) REVERT: N 27 LYS cc_start: -0.1342 (pptt) cc_final: -0.1803 (ptpt) REVERT: N 57 SER cc_start: 0.6675 (m) cc_final: 0.6453 (t) REVERT: N 82 LYS cc_start: 0.7822 (mmpt) cc_final: 0.7479 (mmtm) REVERT: N 92 ILE cc_start: 0.8289 (mt) cc_final: 0.8048 (pt) REVERT: S 78 THR cc_start: 0.6757 (m) cc_final: 0.6515 (p) REVERT: D 30 LYS cc_start: 0.8011 (mmpt) cc_final: 0.7616 (ptmt) REVERT: D 54 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8914 (tp) REVERT: D 69 ARG cc_start: 0.8757 (mmp-170) cc_final: 0.7721 (ptt180) REVERT: D 123 MET cc_start: 0.8248 (ttt) cc_final: 0.7895 (ttt) REVERT: D 147 LYS cc_start: 0.7777 (mttt) cc_final: 0.7552 (mmmt) REVERT: D 194 ILE cc_start: 0.8540 (mt) cc_final: 0.8340 (mp) REVERT: D 195 ASN cc_start: 0.8195 (m-40) cc_final: 0.7855 (t0) REVERT: E 67 ARG cc_start: 0.8556 (ttm110) cc_final: 0.8100 (mtm-85) REVERT: E 94 PHE cc_start: 0.8549 (t80) cc_final: 0.8250 (t80) REVERT: F 9 MET cc_start: 0.5746 (mtt) cc_final: 0.5287 (pmm) REVERT: F 14 GLN cc_start: 0.8766 (tp-100) cc_final: 0.8176 (tp-100) REVERT: F 62 MET cc_start: 0.3074 (mmm) cc_final: 0.2355 (mmm) REVERT: F 68 GLN cc_start: 0.6504 (pm20) cc_final: 0.5229 (mm-40) REVERT: H 9 MET cc_start: 0.8007 (ttp) cc_final: 0.7640 (tmm) REVERT: H 37 ASN cc_start: 0.8262 (t0) cc_final: 0.7978 (m-40) REVERT: L 69 GLU cc_start: 0.7161 (tt0) cc_final: 0.6278 (mm-30) REVERT: L 89 LEU cc_start: 0.8449 (mp) cc_final: 0.8064 (tt) REVERT: O 16 ARG cc_start: 0.7752 (ptp-170) cc_final: 0.7055 (ptt-90) REVERT: O 38 LEU cc_start: 0.8504 (mt) cc_final: 0.7988 (tp) REVERT: O 61 GLN cc_start: 0.8102 (tm-30) cc_final: 0.7677 (tm-30) REVERT: O 64 LYS cc_start: 0.7834 (mtpt) cc_final: 0.7493 (mtpt) REVERT: R 51 GLN cc_start: 0.7521 (pm20) cc_final: 0.6708 (tp40) REVERT: T 26 MET cc_start: 0.8532 (ttp) cc_final: 0.8242 (tmm) REVERT: T 65 LEU cc_start: 0.6364 (OUTLIER) cc_final: 0.5871 (mt) REVERT: B 26 MET cc_start: 0.3141 (tpp) cc_final: 0.2532 (tpp) REVERT: B 44 LYS cc_start: 0.8786 (mmtt) cc_final: 0.7637 (pptt) REVERT: B 56 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6394 (mp) REVERT: B 125 PHE cc_start: 0.3378 (t80) cc_final: 0.3101 (t80) REVERT: B 153 MET cc_start: 0.5234 (ttm) cc_final: 0.3808 (mtp) REVERT: B 183 PHE cc_start: 0.1798 (m-10) cc_final: 0.1533 (m-10) REVERT: B 196 ASP cc_start: 0.6522 (OUTLIER) cc_final: 0.6242 (p0) outliers start: 56 outliers final: 30 residues processed: 421 average time/residue: 0.5709 time to fit residues: 382.4819 Evaluate side-chains 342 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 307 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain T residue 19 HIS Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 196 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 150 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 225 optimal weight: 9.9990 chunk 184 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 272 optimal weight: 6.9990 chunk 293 optimal weight: 30.0000 chunk 242 optimal weight: 0.7980 chunk 269 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 218 optimal weight: 0.0370 overall best weight: 3.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 GLN D 139 ASN ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 GLN L 72 ASN O 37 HIS ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 ASN ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 46213 Z= 0.223 Angle : 0.671 13.238 69052 Z= 0.346 Chirality : 0.039 0.279 8824 Planarity : 0.005 0.068 3762 Dihedral : 24.882 179.902 22895 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.46 % Favored : 86.48 % Rotamer: Outliers : 5.22 % Allowed : 18.89 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -3.93 (0.18), residues: 1716 helix: -2.19 (0.20), residues: 525 sheet: -2.76 (0.32), residues: 230 loop : -2.88 (0.18), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Q 72 HIS 0.010 0.002 HIS O 37 PHE 0.021 0.002 PHE N 20 TYR 0.018 0.002 TYR C 183 ARG 0.011 0.001 ARG T 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 318 time to evaluate : 2.229 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: C 36 PHE cc_start: 0.9047 (t80) cc_final: 0.8735 (t80) REVERT: C 111 ASP cc_start: 0.8330 (t70) cc_final: 0.8038 (t70) REVERT: C 141 MET cc_start: 0.8239 (mmm) cc_final: 0.7743 (tpt) REVERT: C 182 ASP cc_start: 0.7563 (t0) cc_final: 0.7166 (t0) REVERT: J 52 LEU cc_start: 0.9053 (mp) cc_final: 0.8507 (tp) REVERT: N 5 MET cc_start: 0.6215 (tpt) cc_final: 0.5743 (tpp) REVERT: N 27 LYS cc_start: -0.1244 (pptt) cc_final: -0.1569 (ptpt) REVERT: N 57 SER cc_start: 0.7180 (m) cc_final: 0.6754 (t) REVERT: N 92 ILE cc_start: 0.8328 (mt) cc_final: 0.7946 (pt) REVERT: S 65 MET cc_start: -0.0318 (mtt) cc_final: -0.0624 (mtt) REVERT: S 78 THR cc_start: 0.7004 (m) cc_final: 0.6770 (p) REVERT: D 69 ARG cc_start: 0.8832 (mmp-170) cc_final: 0.7757 (ptt180) REVERT: D 74 TYR cc_start: 0.7696 (m-80) cc_final: 0.7314 (m-80) REVERT: D 123 MET cc_start: 0.8364 (ttt) cc_final: 0.7944 (ttt) REVERT: D 147 LYS cc_start: 0.7814 (mttt) cc_final: 0.7604 (mmmt) REVERT: D 194 ILE cc_start: 0.8556 (mt) cc_final: 0.8279 (mp) REVERT: D 195 ASN cc_start: 0.8468 (m-40) cc_final: 0.8002 (t0) REVERT: E 63 MET cc_start: 0.8867 (mmt) cc_final: 0.8652 (mmt) REVERT: E 94 PHE cc_start: 0.8545 (t80) cc_final: 0.8143 (t80) REVERT: E 151 MET cc_start: 0.8291 (mmm) cc_final: 0.7832 (mmm) REVERT: F 9 MET cc_start: 0.5971 (mtt) cc_final: 0.5449 (ppp) REVERT: F 14 GLN cc_start: 0.8746 (tp-100) cc_final: 0.8367 (tp-100) REVERT: F 62 MET cc_start: 0.2968 (mmm) cc_final: 0.2396 (mmm) REVERT: F 68 GLN cc_start: 0.6588 (pm20) cc_final: 0.5432 (mm-40) REVERT: F 88 MET cc_start: 0.7475 (mtt) cc_final: 0.6880 (mpp) REVERT: L 69 GLU cc_start: 0.7013 (tt0) cc_final: 0.6182 (mm-30) REVERT: O 38 LEU cc_start: 0.8490 (mt) cc_final: 0.8046 (tp) REVERT: O 42 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7835 (t80) REVERT: O 61 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7692 (tm-30) REVERT: P 47 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6732 (mm-30) REVERT: R 51 GLN cc_start: 0.7643 (pm20) cc_final: 0.6688 (tp-100) REVERT: R 69 TYR cc_start: 0.1813 (OUTLIER) cc_final: -0.1852 (m-80) REVERT: T 26 MET cc_start: 0.8816 (ttp) cc_final: 0.8486 (tmm) REVERT: T 65 LEU cc_start: 0.6541 (OUTLIER) cc_final: 0.6141 (mt) REVERT: B 44 LYS cc_start: 0.8901 (mmtt) cc_final: 0.8562 (mmmm) REVERT: B 56 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6421 (mp) REVERT: B 183 PHE cc_start: 0.1691 (m-10) cc_final: 0.1412 (m-10) REVERT: B 196 ASP cc_start: 0.6569 (OUTLIER) cc_final: 0.6253 (p0) outliers start: 76 outliers final: 42 residues processed: 364 average time/residue: 0.5687 time to fit residues: 333.0097 Evaluate side-chains 326 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 279 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 65 PHE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 37 HIS Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain R residue 42 ARG Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain T residue 19 HIS Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 220 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 268 optimal weight: 0.0370 chunk 204 optimal weight: 9.9990 chunk 141 optimal weight: 40.0000 chunk 30 optimal weight: 30.0000 chunk 129 optimal weight: 10.0000 chunk 182 optimal weight: 0.4980 chunk 272 optimal weight: 4.9990 chunk 289 optimal weight: 0.5980 chunk 142 optimal weight: 40.0000 chunk 258 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 overall best weight: 2.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN D 70 GLN ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 GLN ** O 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 HIS P 26 ASN R 53 GLN ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 46213 Z= 0.183 Angle : 0.621 12.654 69052 Z= 0.321 Chirality : 0.036 0.272 8824 Planarity : 0.004 0.061 3762 Dihedral : 24.693 179.678 22895 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.53 % Favored : 87.41 % Rotamer: Outliers : 5.08 % Allowed : 20.54 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -3.53 (0.19), residues: 1716 helix: -1.79 (0.21), residues: 533 sheet: -2.34 (0.33), residues: 227 loop : -2.75 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 166 HIS 0.014 0.001 HIS O 37 PHE 0.019 0.002 PHE B 15 TYR 0.022 0.002 TYR C 183 ARG 0.008 0.001 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 306 time to evaluate : 2.290 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: C 36 PHE cc_start: 0.9070 (t80) cc_final: 0.8755 (t80) REVERT: C 111 ASP cc_start: 0.8435 (t70) cc_final: 0.8110 (t70) REVERT: C 182 ASP cc_start: 0.7653 (t0) cc_final: 0.7239 (t0) REVERT: J 52 LEU cc_start: 0.9016 (mp) cc_final: 0.8458 (tp) REVERT: N 5 MET cc_start: 0.6276 (tpt) cc_final: 0.5789 (tpp) REVERT: N 27 LYS cc_start: -0.1283 (pptt) cc_final: -0.1590 (ptpt) REVERT: N 57 SER cc_start: 0.7089 (m) cc_final: 0.6700 (t) REVERT: N 92 ILE cc_start: 0.8319 (mt) cc_final: 0.8033 (pt) REVERT: S 78 THR cc_start: 0.7017 (m) cc_final: 0.6787 (p) REVERT: D 69 ARG cc_start: 0.8791 (mmp-170) cc_final: 0.7767 (ptt180) REVERT: D 74 TYR cc_start: 0.7624 (m-80) cc_final: 0.7259 (m-80) REVERT: D 147 LYS cc_start: 0.7826 (mttt) cc_final: 0.7568 (mmmt) REVERT: D 194 ILE cc_start: 0.8564 (mt) cc_final: 0.8283 (mp) REVERT: D 195 ASN cc_start: 0.8453 (m-40) cc_final: 0.8075 (t0) REVERT: E 18 ASN cc_start: 0.8431 (m110) cc_final: 0.7993 (m-40) REVERT: E 63 MET cc_start: 0.8785 (mmt) cc_final: 0.8567 (mmt) REVERT: E 67 ARG cc_start: 0.8623 (ttm110) cc_final: 0.8175 (ttm110) REVERT: E 68 ARG cc_start: 0.8330 (mmm-85) cc_final: 0.7852 (mmp80) REVERT: E 94 PHE cc_start: 0.8514 (t80) cc_final: 0.8078 (t80) REVERT: F 1 MET cc_start: 0.6014 (ttm) cc_final: 0.5549 (tpp) REVERT: F 14 GLN cc_start: 0.8687 (tp-100) cc_final: 0.8315 (tp-100) REVERT: F 62 MET cc_start: 0.2915 (mmm) cc_final: 0.2362 (mmm) REVERT: F 68 GLN cc_start: 0.6753 (pm20) cc_final: 0.5847 (mm-40) REVERT: F 88 MET cc_start: 0.7556 (mtt) cc_final: 0.6994 (mpp) REVERT: H 2 MET cc_start: 0.4882 (tpt) cc_final: 0.4653 (tpt) REVERT: H 30 LYS cc_start: 0.8096 (mmpt) cc_final: 0.7524 (mptt) REVERT: H 41 GLU cc_start: 0.8365 (mp0) cc_final: 0.8102 (mp0) REVERT: H 63 LYS cc_start: 0.6166 (tttt) cc_final: 0.5488 (tppt) REVERT: H 64 TYR cc_start: 0.7503 (OUTLIER) cc_final: 0.6555 (p90) REVERT: L 69 GLU cc_start: 0.7115 (tt0) cc_final: 0.6176 (mm-30) REVERT: L 89 LEU cc_start: 0.8399 (mp) cc_final: 0.8058 (tt) REVERT: O 38 LEU cc_start: 0.8496 (mt) cc_final: 0.8061 (tt) REVERT: O 42 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7813 (t80) REVERT: O 61 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7618 (tm-30) REVERT: O 70 LYS cc_start: 0.9035 (mmmt) cc_final: 0.8662 (mmmm) REVERT: Q 8 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7613 (mm-40) REVERT: R 51 GLN cc_start: 0.7647 (pm20) cc_final: 0.6761 (tp-100) REVERT: T 65 LEU cc_start: 0.6432 (OUTLIER) cc_final: 0.6042 (mt) REVERT: B 29 PHE cc_start: 0.8183 (m-80) cc_final: 0.7522 (t80) REVERT: B 44 LYS cc_start: 0.8915 (mmtt) cc_final: 0.8638 (mmmm) REVERT: B 183 PHE cc_start: 0.1694 (m-10) cc_final: 0.1349 (m-10) outliers start: 74 outliers final: 45 residues processed: 348 average time/residue: 0.5547 time to fit residues: 312.3657 Evaluate side-chains 327 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 278 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 65 PHE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 83 ARG Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 8 GLN Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain R residue 42 ARG Chi-restraints excluded: chain T residue 19 HIS Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 196 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 240 optimal weight: 0.7980 chunk 164 optimal weight: 30.0000 chunk 4 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 119 optimal weight: 30.0000 chunk 246 optimal weight: 9.9990 chunk 199 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 259 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN D 73 ASN E 147 ASN ** O 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 HIS ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 46213 Z= 0.210 Angle : 0.637 12.010 69052 Z= 0.328 Chirality : 0.037 0.280 8824 Planarity : 0.005 0.064 3762 Dihedral : 24.677 179.952 22895 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.29 % Favored : 86.66 % Rotamer: Outliers : 5.49 % Allowed : 21.77 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -3.44 (0.19), residues: 1716 helix: -1.70 (0.21), residues: 539 sheet: -2.29 (0.33), residues: 238 loop : -2.69 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 166 HIS 0.006 0.001 HIS J 15 PHE 0.016 0.002 PHE O 42 TYR 0.038 0.002 TYR C 167 ARG 0.008 0.001 ARG D 145 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 291 time to evaluate : 2.438 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: C 36 PHE cc_start: 0.9062 (t80) cc_final: 0.8751 (t80) REVERT: C 111 ASP cc_start: 0.8579 (t70) cc_final: 0.8235 (t70) REVERT: C 182 ASP cc_start: 0.7778 (t0) cc_final: 0.7382 (t0) REVERT: J 42 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.6587 (mt) REVERT: J 52 LEU cc_start: 0.9032 (mp) cc_final: 0.8471 (tp) REVERT: N 5 MET cc_start: 0.6437 (tpt) cc_final: 0.5959 (tpp) REVERT: N 27 LYS cc_start: -0.1246 (pptt) cc_final: -0.1585 (ptpt) REVERT: N 57 SER cc_start: 0.7440 (m) cc_final: 0.7139 (t) REVERT: N 92 ILE cc_start: 0.8357 (mt) cc_final: 0.8049 (pt) REVERT: S 78 THR cc_start: 0.6999 (m) cc_final: 0.6752 (p) REVERT: D 69 ARG cc_start: 0.8820 (mmp-170) cc_final: 0.7805 (ptt180) REVERT: D 74 TYR cc_start: 0.7666 (m-80) cc_final: 0.7333 (m-80) REVERT: D 123 MET cc_start: 0.8443 (tpp) cc_final: 0.8242 (tpp) REVERT: D 147 LYS cc_start: 0.7672 (mttt) cc_final: 0.7452 (mmmt) REVERT: D 194 ILE cc_start: 0.8576 (mt) cc_final: 0.8294 (mp) REVERT: D 195 ASN cc_start: 0.8433 (m-40) cc_final: 0.8152 (t0) REVERT: E 18 ASN cc_start: 0.8449 (m110) cc_final: 0.8008 (m-40) REVERT: E 63 MET cc_start: 0.8737 (mmt) cc_final: 0.8494 (mmt) REVERT: E 67 ARG cc_start: 0.8693 (ttm110) cc_final: 0.8263 (ttm110) REVERT: E 94 PHE cc_start: 0.8554 (t80) cc_final: 0.8036 (t80) REVERT: E 151 MET cc_start: 0.8311 (tpp) cc_final: 0.7916 (tpp) REVERT: F 1 MET cc_start: 0.6169 (ttm) cc_final: 0.5680 (tpp) REVERT: F 14 GLN cc_start: 0.8622 (tp-100) cc_final: 0.8238 (tp-100) REVERT: F 24 ARG cc_start: 0.8295 (ttm110) cc_final: 0.7860 (mtm110) REVERT: F 62 MET cc_start: 0.2684 (mmm) cc_final: 0.2077 (mmm) REVERT: F 68 GLN cc_start: 0.6750 (pm20) cc_final: 0.5794 (mt0) REVERT: F 74 LEU cc_start: 0.9484 (mm) cc_final: 0.9230 (mm) REVERT: F 88 MET cc_start: 0.7717 (mtt) cc_final: 0.7180 (mpp) REVERT: H 15 ASN cc_start: 0.5895 (OUTLIER) cc_final: 0.5446 (t0) REVERT: H 30 LYS cc_start: 0.8055 (mmpt) cc_final: 0.7493 (mptt) REVERT: H 63 LYS cc_start: 0.6133 (tttt) cc_final: 0.5431 (tppt) REVERT: H 64 TYR cc_start: 0.7633 (OUTLIER) cc_final: 0.6742 (p90) REVERT: L 69 GLU cc_start: 0.7079 (tt0) cc_final: 0.6142 (mm-30) REVERT: L 89 LEU cc_start: 0.8458 (mp) cc_final: 0.8031 (tt) REVERT: O 38 LEU cc_start: 0.8443 (mt) cc_final: 0.7968 (tp) REVERT: O 42 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7864 (t80) REVERT: O 58 MET cc_start: 0.8229 (ptp) cc_final: 0.8016 (ptp) REVERT: O 61 GLN cc_start: 0.8356 (tm-30) cc_final: 0.7669 (tm-30) REVERT: Q 8 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7756 (mm-40) REVERT: R 51 GLN cc_start: 0.7593 (pm20) cc_final: 0.6643 (tp-100) REVERT: T 65 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.6249 (mt) REVERT: B 29 PHE cc_start: 0.7965 (m-80) cc_final: 0.7600 (p90) REVERT: B 44 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8678 (mmmm) REVERT: B 114 LYS cc_start: 0.6881 (tppt) cc_final: 0.6640 (mmmt) REVERT: B 196 ASP cc_start: 0.6458 (OUTLIER) cc_final: 0.6165 (p0) REVERT: B 203 ASP cc_start: 0.6862 (OUTLIER) cc_final: 0.6289 (p0) outliers start: 80 outliers final: 55 residues processed: 337 average time/residue: 0.5845 time to fit residues: 319.6062 Evaluate side-chains 342 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 279 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain H residue 15 ASN Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 65 PHE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 37 HIS Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 83 ARG Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 8 GLN Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain R residue 42 ARG Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain T residue 19 HIS Chi-restraints excluded: chain T residue 38 ILE Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 220 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 97 optimal weight: 10.0000 chunk 260 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 169 optimal weight: 50.0000 chunk 71 optimal weight: 10.0000 chunk 289 optimal weight: 10.0000 chunk 240 optimal weight: 0.8980 chunk 133 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 151 optimal weight: 40.0000 overall best weight: 7.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 ASN D 70 GLN L 4 ASN ** O 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 HIS ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 74 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.138 46213 Z= 0.411 Angle : 0.851 10.958 69052 Z= 0.429 Chirality : 0.045 0.320 8824 Planarity : 0.006 0.092 3762 Dihedral : 25.036 179.567 22895 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 30.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 16.14 % Favored : 83.80 % Rotamer: Outliers : 6.59 % Allowed : 22.53 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -3.59 (0.19), residues: 1716 helix: -1.93 (0.21), residues: 538 sheet: -2.46 (0.32), residues: 243 loop : -2.69 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP Q 72 HIS 0.030 0.003 HIS O 37 PHE 0.026 0.003 PHE C 129 TYR 0.020 0.003 TYR H 64 ARG 0.008 0.001 ARG D 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 274 time to evaluate : 1.950 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: C 36 PHE cc_start: 0.9048 (t80) cc_final: 0.8778 (t80) REVERT: C 130 ARG cc_start: 0.7226 (tmm-80) cc_final: 0.6129 (tmt170) REVERT: C 133 MET cc_start: 0.7957 (ptp) cc_final: 0.7530 (ptp) REVERT: C 182 ASP cc_start: 0.7700 (t0) cc_final: 0.7397 (m-30) REVERT: J 52 LEU cc_start: 0.9022 (mp) cc_final: 0.8457 (tp) REVERT: N 5 MET cc_start: 0.6622 (tpt) cc_final: 0.6249 (tpp) REVERT: N 57 SER cc_start: 0.7419 (m) cc_final: 0.7105 (t) REVERT: N 95 LEU cc_start: 0.6619 (tp) cc_final: 0.6331 (tp) REVERT: S 28 LYS cc_start: 0.4973 (OUTLIER) cc_final: 0.4723 (pmmt) REVERT: S 65 MET cc_start: 0.0053 (mtm) cc_final: -0.0437 (mtt) REVERT: S 78 THR cc_start: 0.6861 (m) cc_final: 0.6615 (p) REVERT: D 74 TYR cc_start: 0.7864 (m-80) cc_final: 0.7449 (m-80) REVERT: D 147 LYS cc_start: 0.7696 (mttt) cc_final: 0.7376 (mmtt) REVERT: D 194 ILE cc_start: 0.8579 (mt) cc_final: 0.8204 (mp) REVERT: E 18 ASN cc_start: 0.8455 (m110) cc_final: 0.8100 (m-40) REVERT: E 67 ARG cc_start: 0.8766 (ttm110) cc_final: 0.8510 (ttm110) REVERT: E 94 PHE cc_start: 0.8627 (t80) cc_final: 0.8155 (t80) REVERT: E 96 GLN cc_start: 0.8841 (tp40) cc_final: 0.8621 (tp40) REVERT: E 151 MET cc_start: 0.8534 (tpp) cc_final: 0.8114 (tpp) REVERT: F 1 MET cc_start: 0.6560 (ttm) cc_final: 0.5869 (tpp) REVERT: F 21 MET cc_start: 0.7113 (tpt) cc_final: 0.6897 (tpt) REVERT: F 24 ARG cc_start: 0.8154 (ttm110) cc_final: 0.7713 (mtm110) REVERT: F 62 MET cc_start: 0.2859 (mmm) cc_final: 0.2332 (mmm) REVERT: F 68 GLN cc_start: 0.6961 (pm20) cc_final: 0.5809 (mm-40) REVERT: F 88 MET cc_start: 0.7668 (mtt) cc_final: 0.7200 (mpp) REVERT: H 30 LYS cc_start: 0.8255 (mmpt) cc_final: 0.7627 (mptt) REVERT: H 64 TYR cc_start: 0.7492 (OUTLIER) cc_final: 0.6342 (p90) REVERT: O 38 LEU cc_start: 0.8424 (mt) cc_final: 0.8063 (tp) REVERT: O 58 MET cc_start: 0.8287 (ptp) cc_final: 0.8015 (ptp) REVERT: O 61 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8229 (tm-30) REVERT: O 80 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7877 (tt) REVERT: Q 59 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7101 (mm-30) REVERT: B 26 MET cc_start: 0.1257 (mmp) cc_final: 0.0769 (mmp) REVERT: B 29 PHE cc_start: 0.8137 (m-80) cc_final: 0.7627 (p90) REVERT: B 196 ASP cc_start: 0.6504 (OUTLIER) cc_final: 0.6189 (p0) outliers start: 96 outliers final: 67 residues processed: 333 average time/residue: 0.5433 time to fit residues: 296.0486 Evaluate side-chains 323 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 252 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain H residue 15 ASN Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 8 GLN Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 42 ARG Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain T residue 19 HIS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 220 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 278 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 164 optimal weight: 30.0000 chunk 211 optimal weight: 1.9990 chunk 163 optimal weight: 30.0000 chunk 243 optimal weight: 3.9990 chunk 161 optimal weight: 50.0000 chunk 288 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 175 optimal weight: 30.0000 chunk 133 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 GLN ** O 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 HIS ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 59 HIS ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 46213 Z= 0.237 Angle : 0.680 12.439 69052 Z= 0.350 Chirality : 0.039 0.330 8824 Planarity : 0.005 0.078 3762 Dihedral : 24.792 179.843 22895 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.10 % Favored : 85.84 % Rotamer: Outliers : 5.36 % Allowed : 25.55 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -3.19 (0.19), residues: 1716 helix: -1.39 (0.22), residues: 523 sheet: -2.10 (0.35), residues: 217 loop : -2.63 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 72 HIS 0.008 0.001 HIS J 15 PHE 0.035 0.002 PHE H 65 TYR 0.013 0.002 TYR L 65 ARG 0.007 0.001 ARG T 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 279 time to evaluate : 2.614 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: C 36 PHE cc_start: 0.9036 (t80) cc_final: 0.8684 (t80) REVERT: C 167 TYR cc_start: 0.5608 (m-80) cc_final: 0.5056 (m-80) REVERT: C 182 ASP cc_start: 0.7840 (t0) cc_final: 0.7382 (t0) REVERT: J 52 LEU cc_start: 0.9004 (mp) cc_final: 0.8431 (tp) REVERT: N 5 MET cc_start: 0.6564 (tpt) cc_final: 0.6220 (tpp) REVERT: N 19 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7897 (m-10) REVERT: N 57 SER cc_start: 0.7462 (m) cc_final: 0.7090 (t) REVERT: N 91 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7244 (mt-10) REVERT: N 92 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8310 (pt) REVERT: S 65 MET cc_start: -0.0263 (mtm) cc_final: -0.0777 (mtt) REVERT: S 78 THR cc_start: 0.6765 (m) cc_final: 0.6496 (p) REVERT: D 74 TYR cc_start: 0.7747 (m-80) cc_final: 0.7505 (m-80) REVERT: E 67 ARG cc_start: 0.8738 (ttm110) cc_final: 0.8331 (ttm110) REVERT: E 68 ARG cc_start: 0.8537 (mmm-85) cc_final: 0.7922 (mmp80) REVERT: E 94 PHE cc_start: 0.8587 (t80) cc_final: 0.8161 (t80) REVERT: E 151 MET cc_start: 0.8450 (tpp) cc_final: 0.8070 (tpp) REVERT: F 1 MET cc_start: 0.6247 (ttm) cc_final: 0.5744 (tpp) REVERT: F 21 MET cc_start: 0.7055 (tpt) cc_final: 0.6815 (tpt) REVERT: F 24 ARG cc_start: 0.8206 (ttm110) cc_final: 0.7821 (mtm110) REVERT: F 62 MET cc_start: 0.2769 (mmm) cc_final: 0.2165 (mmm) REVERT: F 68 GLN cc_start: 0.6865 (pm20) cc_final: 0.5919 (mt0) REVERT: F 88 MET cc_start: 0.7944 (mtt) cc_final: 0.7365 (mpp) REVERT: H 30 LYS cc_start: 0.8133 (mmpt) cc_final: 0.7926 (ttpt) REVERT: H 63 LYS cc_start: 0.5976 (tttt) cc_final: 0.5153 (tppt) REVERT: H 64 TYR cc_start: 0.7190 (OUTLIER) cc_final: 0.6079 (p90) REVERT: O 42 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7866 (t80) REVERT: O 58 MET cc_start: 0.8251 (ptp) cc_final: 0.8008 (ptp) REVERT: O 61 GLN cc_start: 0.8417 (tm-30) cc_final: 0.8199 (tm-30) REVERT: Q 8 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7751 (mm-40) REVERT: B 26 MET cc_start: 0.1596 (mmp) cc_final: 0.1297 (mmp) REVERT: B 29 PHE cc_start: 0.8268 (m-80) cc_final: 0.7645 (p90) REVERT: B 99 MET cc_start: 0.5979 (mtt) cc_final: 0.5744 (ttm) REVERT: B 196 ASP cc_start: 0.6264 (OUTLIER) cc_final: 0.5973 (p0) outliers start: 78 outliers final: 63 residues processed: 325 average time/residue: 0.5473 time to fit residues: 291.5011 Evaluate side-chains 329 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 260 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain N residue 19 TYR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 8 GLN Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain R residue 42 ARG Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain T residue 19 HIS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 220 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 178 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 chunk 172 optimal weight: 40.0000 chunk 86 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 196 optimal weight: 6.9990 chunk 142 optimal weight: 40.0000 chunk 26 optimal weight: 5.9990 chunk 226 optimal weight: 0.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 59 HIS ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 46213 Z= 0.298 Angle : 0.721 15.053 69052 Z= 0.368 Chirality : 0.040 0.347 8824 Planarity : 0.005 0.096 3762 Dihedral : 24.814 179.459 22895 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 24.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.39 % Favored : 85.55 % Rotamer: Outliers : 5.49 % Allowed : 26.24 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -3.20 (0.20), residues: 1716 helix: -1.39 (0.22), residues: 523 sheet: -2.22 (0.34), residues: 227 loop : -2.59 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 103 HIS 0.013 0.002 HIS B 93 PHE 0.035 0.002 PHE H 65 TYR 0.015 0.002 TYR L 65 ARG 0.006 0.001 ARG C 130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 262 time to evaluate : 2.431 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: C 36 PHE cc_start: 0.9036 (t80) cc_final: 0.8726 (t80) REVERT: C 167 TYR cc_start: 0.4950 (m-80) cc_final: 0.4566 (m-80) REVERT: C 182 ASP cc_start: 0.7922 (t0) cc_final: 0.7529 (m-30) REVERT: J 52 LEU cc_start: 0.9000 (mp) cc_final: 0.8446 (tp) REVERT: N 5 MET cc_start: 0.6582 (tpt) cc_final: 0.6232 (tpp) REVERT: N 19 TYR cc_start: 0.8190 (OUTLIER) cc_final: 0.7898 (m-10) REVERT: N 57 SER cc_start: 0.7502 (m) cc_final: 0.7135 (t) REVERT: N 91 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7263 (mt-10) REVERT: N 92 ILE cc_start: 0.8554 (mt) cc_final: 0.8289 (pt) REVERT: S 28 LYS cc_start: 0.4969 (OUTLIER) cc_final: 0.4746 (pmmt) REVERT: S 65 MET cc_start: -0.0039 (mtm) cc_final: -0.0542 (mtt) REVERT: S 78 THR cc_start: 0.6770 (m) cc_final: 0.6494 (p) REVERT: D 74 TYR cc_start: 0.7763 (m-80) cc_final: 0.7502 (m-80) REVERT: D 123 MET cc_start: 0.8532 (tpp) cc_final: 0.8311 (tpp) REVERT: E 67 ARG cc_start: 0.8731 (ttm110) cc_final: 0.8442 (ttm110) REVERT: E 94 PHE cc_start: 0.8612 (t80) cc_final: 0.8129 (t80) REVERT: E 151 MET cc_start: 0.8433 (tpp) cc_final: 0.8042 (tpp) REVERT: F 1 MET cc_start: 0.6421 (ttm) cc_final: 0.5846 (tpp) REVERT: F 24 ARG cc_start: 0.8219 (ttm110) cc_final: 0.7857 (mtm110) REVERT: F 62 MET cc_start: 0.2670 (mmm) cc_final: 0.2112 (mmm) REVERT: F 68 GLN cc_start: 0.6886 (pm20) cc_final: 0.5912 (mt0) REVERT: F 88 MET cc_start: 0.7917 (mtt) cc_final: 0.7352 (mpp) REVERT: H 15 ASN cc_start: 0.6177 (OUTLIER) cc_final: 0.5519 (t0) REVERT: H 30 LYS cc_start: 0.8143 (mmpt) cc_final: 0.7935 (ttpt) REVERT: H 63 LYS cc_start: 0.6000 (tttt) cc_final: 0.5134 (tppt) REVERT: H 64 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.6391 (p90) REVERT: O 42 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.7986 (t80) REVERT: O 53 ARG cc_start: 0.6763 (OUTLIER) cc_final: 0.6545 (ttp-170) REVERT: O 61 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8194 (tm-30) REVERT: Q 8 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7758 (mm-40) REVERT: B 29 PHE cc_start: 0.8266 (m-80) cc_final: 0.7661 (p90) REVERT: B 196 ASP cc_start: 0.6277 (OUTLIER) cc_final: 0.5977 (p0) outliers start: 80 outliers final: 64 residues processed: 310 average time/residue: 0.5439 time to fit residues: 275.2677 Evaluate side-chains 328 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 256 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain N residue 19 TYR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain H residue 15 ASN Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 53 ARG Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 8 GLN Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain R residue 42 ARG Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain T residue 19 HIS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 220 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 262 optimal weight: 3.9990 chunk 276 optimal weight: 6.9990 chunk 251 optimal weight: 10.0000 chunk 268 optimal weight: 20.0000 chunk 161 optimal weight: 50.0000 chunk 116 optimal weight: 10.0000 chunk 210 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 242 optimal weight: 1.9990 chunk 253 optimal weight: 0.7980 chunk 267 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 GLN L 72 ASN O 27 GLN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN B 92 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 46213 Z= 0.199 Angle : 0.640 14.446 69052 Z= 0.329 Chirality : 0.037 0.330 8824 Planarity : 0.005 0.073 3762 Dihedral : 24.645 179.574 22895 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.65 % Favored : 87.30 % Rotamer: Outliers : 5.29 % Allowed : 26.44 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -3.00 (0.20), residues: 1716 helix: -1.18 (0.23), residues: 523 sheet: -2.17 (0.34), residues: 235 loop : -2.47 (0.19), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP P 60 HIS 0.023 0.001 HIS P 59 PHE 0.041 0.002 PHE H 65 TYR 0.013 0.001 TYR L 65 ARG 0.006 0.000 ARG P 56 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 283 time to evaluate : 2.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 PHE cc_start: 0.9054 (t80) cc_final: 0.8734 (t80) REVERT: C 167 TYR cc_start: 0.5303 (m-80) cc_final: 0.4804 (m-80) REVERT: C 182 ASP cc_start: 0.7999 (t0) cc_final: 0.7556 (t0) REVERT: J 52 LEU cc_start: 0.8978 (mp) cc_final: 0.8425 (tp) REVERT: N 5 MET cc_start: 0.6519 (tpt) cc_final: 0.6146 (tpp) REVERT: N 19 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7901 (m-10) REVERT: N 57 SER cc_start: 0.7428 (m) cc_final: 0.7050 (t) REVERT: N 91 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7286 (mt-10) REVERT: N 92 ILE cc_start: 0.8543 (mt) cc_final: 0.8237 (pt) REVERT: S 28 LYS cc_start: 0.5085 (OUTLIER) cc_final: 0.4865 (pmmt) REVERT: S 65 MET cc_start: -0.0314 (mtm) cc_final: -0.0851 (mtt) REVERT: S 78 THR cc_start: 0.6808 (m) cc_final: 0.6519 (p) REVERT: D 30 LYS cc_start: 0.7954 (mmpt) cc_final: 0.7316 (ptmt) REVERT: D 123 MET cc_start: 0.8367 (tpp) cc_final: 0.7248 (tpp) REVERT: E 67 ARG cc_start: 0.8674 (ttm110) cc_final: 0.8220 (ttm110) REVERT: E 68 ARG cc_start: 0.8476 (mmm-85) cc_final: 0.7871 (mmp80) REVERT: E 94 PHE cc_start: 0.8582 (t80) cc_final: 0.7941 (t80) REVERT: E 156 ARG cc_start: 0.6030 (ttm170) cc_final: 0.5640 (ttp-170) REVERT: F 1 MET cc_start: 0.6190 (ttm) cc_final: 0.5783 (tpp) REVERT: F 24 ARG cc_start: 0.8085 (ttm110) cc_final: 0.7788 (mtm110) REVERT: F 62 MET cc_start: 0.2767 (mmm) cc_final: 0.2247 (mmm) REVERT: F 68 GLN cc_start: 0.6951 (pm20) cc_final: 0.6181 (mt0) REVERT: F 88 MET cc_start: 0.7881 (mtt) cc_final: 0.7355 (mpp) REVERT: H 63 LYS cc_start: 0.5918 (tttt) cc_final: 0.5070 (tppt) REVERT: H 64 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.5887 (p90) REVERT: O 3 SER cc_start: 0.8427 (m) cc_final: 0.7975 (p) REVERT: O 58 MET cc_start: 0.8320 (ptp) cc_final: 0.8042 (ptp) REVERT: O 61 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8169 (tm-30) REVERT: O 70 LYS cc_start: 0.9071 (mmtt) cc_final: 0.8453 (mmtm) REVERT: Q 8 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7815 (mm-40) REVERT: B 26 MET cc_start: 0.1388 (mmp) cc_final: 0.0419 (mmp) REVERT: B 29 PHE cc_start: 0.8307 (m-80) cc_final: 0.7715 (p90) REVERT: B 99 MET cc_start: 0.5722 (mtt) cc_final: 0.5465 (ttm) REVERT: B 196 ASP cc_start: 0.6360 (OUTLIER) cc_final: 0.6109 (p0) outliers start: 77 outliers final: 61 residues processed: 329 average time/residue: 0.5479 time to fit residues: 294.0581 Evaluate side-chains 334 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 268 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain N residue 19 TYR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 8 GLN Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain T residue 19 HIS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 220 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 176 optimal weight: 30.0000 chunk 283 optimal weight: 30.0000 chunk 173 optimal weight: 30.0000 chunk 134 optimal weight: 20.0000 chunk 197 optimal weight: 4.9990 chunk 297 optimal weight: 9.9990 chunk 274 optimal weight: 9.9990 chunk 237 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 183 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN E 145 ASN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 59 HIS ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN B 93 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.133 46213 Z= 0.420 Angle : 0.871 14.568 69052 Z= 0.439 Chirality : 0.046 0.368 8824 Planarity : 0.006 0.092 3762 Dihedral : 25.069 179.817 22895 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 31.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 17.25 % Favored : 82.69 % Rotamer: Outliers : 5.15 % Allowed : 26.44 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -3.40 (0.19), residues: 1716 helix: -1.72 (0.21), residues: 530 sheet: -2.39 (0.33), residues: 233 loop : -2.60 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP Q 72 HIS 0.013 0.002 HIS J 15 PHE 0.045 0.003 PHE H 65 TYR 0.020 0.003 TYR D 74 ARG 0.009 0.001 ARG D 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 252 time to evaluate : 2.350 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: C 36 PHE cc_start: 0.8995 (t80) cc_final: 0.8711 (t80) REVERT: C 167 TYR cc_start: 0.5237 (m-80) cc_final: 0.4762 (m-80) REVERT: C 182 ASP cc_start: 0.7907 (t0) cc_final: 0.7484 (t0) REVERT: J 52 LEU cc_start: 0.8994 (mp) cc_final: 0.8442 (tp) REVERT: N 5 MET cc_start: 0.6769 (tpt) cc_final: 0.6347 (tpp) REVERT: N 19 TYR cc_start: 0.8180 (OUTLIER) cc_final: 0.7877 (m-10) REVERT: N 57 SER cc_start: 0.7423 (m) cc_final: 0.7077 (t) REVERT: N 91 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7295 (mt-10) REVERT: N 95 LEU cc_start: 0.6631 (tp) cc_final: 0.6427 (tp) REVERT: S 28 LYS cc_start: 0.4989 (OUTLIER) cc_final: 0.4753 (pmmt) REVERT: S 65 MET cc_start: 0.0228 (mtm) cc_final: -0.0238 (mtt) REVERT: S 78 THR cc_start: 0.6640 (m) cc_final: 0.6363 (p) REVERT: D 147 LYS cc_start: 0.7864 (mttt) cc_final: 0.7617 (tttt) REVERT: E 67 ARG cc_start: 0.8768 (ttm110) cc_final: 0.8479 (ttm110) REVERT: E 94 PHE cc_start: 0.8644 (t80) cc_final: 0.8266 (t80) REVERT: F 1 MET cc_start: 0.6692 (ttm) cc_final: 0.6007 (tpp) REVERT: F 24 ARG cc_start: 0.8150 (ttm110) cc_final: 0.7833 (mtm110) REVERT: F 68 GLN cc_start: 0.7095 (pm20) cc_final: 0.6026 (mm-40) REVERT: H 64 TYR cc_start: 0.7496 (OUTLIER) cc_final: 0.6494 (p90) REVERT: O 3 SER cc_start: 0.8491 (m) cc_final: 0.7972 (p) REVERT: O 58 MET cc_start: 0.8338 (ptp) cc_final: 0.8091 (ptp) REVERT: O 70 LYS cc_start: 0.8958 (mmtt) cc_final: 0.8420 (mmtm) REVERT: Q 8 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7636 (mm-40) REVERT: Q 79 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8510 (mm-30) REVERT: B 29 PHE cc_start: 0.8288 (m-80) cc_final: 0.7664 (p90) REVERT: B 196 ASP cc_start: 0.6208 (OUTLIER) cc_final: 0.5990 (p0) outliers start: 75 outliers final: 64 residues processed: 299 average time/residue: 0.5486 time to fit residues: 269.7327 Evaluate side-chains 313 residues out of total 1458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 244 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain N residue 19 TYR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 8 PHE Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 8 GLN Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain T residue 19 HIS Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 220 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 188 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 218 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 65 optimal weight: 20.0000 chunk 237 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 243 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 ASN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 59 HIS ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 ASN B 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.102049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.077581 restraints weight = 192198.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.079681 restraints weight = 69067.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.080031 restraints weight = 37881.024| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 46213 Z= 0.200 Angle : 0.666 14.338 69052 Z= 0.341 Chirality : 0.037 0.323 8824 Planarity : 0.005 0.078 3762 Dihedral : 24.721 179.198 22895 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.05 % Favored : 86.89 % Rotamer: Outliers : 4.88 % Allowed : 27.06 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -2.99 (0.20), residues: 1716 helix: -1.19 (0.23), residues: 521 sheet: -2.13 (0.35), residues: 229 loop : -2.47 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 103 HIS 0.026 0.001 HIS B 93 PHE 0.021 0.002 PHE H 65 TYR 0.013 0.002 TYR L 65 ARG 0.004 0.000 ARG C 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7062.30 seconds wall clock time: 130 minutes 16.86 seconds (7816.86 seconds total)