Starting phenix.real_space_refine on Tue Nov 19 18:39:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c94_16501/11_2024/8c94_16501.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c94_16501/11_2024/8c94_16501.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/8c94_16501/11_2024/8c94_16501.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c94_16501/11_2024/8c94_16501.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c94_16501/11_2024/8c94_16501.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c94_16501/11_2024/8c94_16501.cif" } 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= 0.003 sd= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1787 5.49 5 S 45 5.16 5 C 27261 2.51 5 N 10205 2.21 5 O 15262 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 54560 Number of models: 1 Model: "" Number of chains: 21 Chain: "0" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 429 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "2" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 315 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'TRANS': 38} Chain: "A" Number of atoms: 35860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1668, 35860 Classifications: {'RNA': 1668} Modifications used: {'rna2p_pur': 164, 'rna2p_pyr': 83, 'rna3p_pur': 819, 'rna3p_pyr': 602} Link IDs: {'rna2p': 247, 'rna3p': 1420} Chain breaks: 10 Chain: "B" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Chain: "D" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1335 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain breaks: 1 Chain: "E" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1481 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 186} Chain breaks: 1 Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 808 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 1 Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 781 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain breaks: 1 Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 513 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 66} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 499 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Time building chain proxies: 27.92, per 1000 atoms: 0.51 Number of scatterers: 54560 At special positions: 0 Unit cell: (183.75, 216.25, 205, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 1787 15.00 O 15262 8.00 N 10205 7.00 C 27261 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 - 3.00 Amino acid : True - 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: 12.50 Conformation dependent library (CDL) restraints added in 2.7 seconds 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3798 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 25 sheets defined 34.2% alpha, 18.5% beta 593 base pairs and 822 stacking pairs defined. Time for finding SS restraints: 24.49 Creating SS restraints... Processing helix chain '0' and resid 8 through 16 Processing helix chain '0' and resid 17 through 20 removed outlier: 3.974A pdb=" N ALA 0 20 " --> pdb=" O SER 0 17 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 17 through 20' Processing helix chain '2' and resid 9 through 17 Processing helix chain '2' and resid 17 through 22 Processing helix chain '2' and resid 24 through 38 Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 61 through 72 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.562A pdb=" N LEU D 100 " --> pdb=" O SER D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'E' and resid 15 through 21 removed outlier: 3.551A pdb=" N ARG E 21 " --> pdb=" O THR E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 39 Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 141 removed outlier: 3.536A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 160 Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 190 through 201 removed outlier: 4.167A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 20 removed outlier: 3.833A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LYS F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS F 14 " --> pdb=" O GLU F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 27 removed outlier: 3.957A pdb=" N VAL F 27 " --> pdb=" O VAL F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 44 removed outlier: 4.274A pdb=" N ALA F 44 " --> pdb=" O GLU F 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 41 through 44' Processing helix chain 'F' and resid 45 through 60 removed outlier: 4.328A pdb=" N LEU F 49 " --> pdb=" O ASP F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 105 removed outlier: 3.938A pdb=" N TRP F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 137 Processing helix chain 'F' and resid 141 through 145 Processing helix chain 'F' and resid 161 through 172 removed outlier: 3.536A pdb=" N GLY F 165 " --> pdb=" O SER F 161 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 58 through 62 removed outlier: 3.831A pdb=" N VAL J 62 " --> pdb=" O ALA J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 89 through 96 Processing helix chain 'J' and resid 96 through 107 removed outlier: 3.947A pdb=" N VAL J 100 " --> pdb=" O ARG J 96 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 122 removed outlier: 3.788A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 136 Processing helix chain 'K' and resid 109 through 111 No H-bonds generated for 'chain 'K' and resid 109 through 111' Processing helix chain 'K' and resid 112 through 118 Processing helix chain 'L' and resid 2 through 6 removed outlier: 3.899A pdb=" N LEU L 6 " --> pdb=" O LEU L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 138 Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 37 through 56 removed outlier: 3.755A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 69 removed outlier: 3.685A pdb=" N ARG N 69 " --> pdb=" O LEU N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 79 Processing helix chain 'N' and resid 82 through 87 Processing helix chain 'O' and resid 3 through 20 removed outlier: 3.873A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 115 removed outlier: 3.830A pdb=" N ALA O 105 " --> pdb=" O GLY O 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 12 Processing helix chain 'P' and resid 52 through 55 Processing helix chain 'P' and resid 96 through 101 Processing helix chain 'P' and resid 103 through 108 Processing helix chain 'Q' and resid 5 through 19 removed outlier: 3.579A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 3.616A pdb=" N VAL Q 30 " --> pdb=" O ALA Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 71 removed outlier: 4.194A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 101 through 117 Processing helix chain 'S' and resid 14 through 22 removed outlier: 3.998A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 25 No H-bonds generated for 'chain 'S' and resid 23 through 25' Processing helix chain 'S' and resid 28 through 38 Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.640A pdb=" N LYS S 49 " --> pdb=" O VAL S 45 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 69 removed outlier: 3.815A pdb=" N ASP S 68 " --> pdb=" O ASP S 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 23 removed outlier: 3.696A pdb=" N SER V 17 " --> pdb=" O GLY V 13 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 50 Processing helix chain 'V' and resid 51 through 52 No H-bonds generated for 'chain 'V' and resid 51 through 52' Processing helix chain 'V' and resid 53 through 58 Processing helix chain 'Y' and resid 9 through 34 removed outlier: 3.618A pdb=" N GLU Y 13 " --> pdb=" O LYS Y 9 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 44 removed outlier: 4.078A pdb=" N LEU Y 42 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU Y 43 " --> pdb=" O SER Y 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 48 through 56 removed outlier: 3.809A pdb=" N LEU Y 56 " --> pdb=" O ARG Y 52 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 Processing sheet with id=AA1, first strand: chain '0' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain 'D' and resid 169 through 175 removed outlier: 5.219A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG D 179 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LYS D 190 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL D 177 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 78 through 83 removed outlier: 3.874A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN D 36 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE D 96 " --> pdb=" O ASN D 32 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.420A pdb=" N ILE E 119 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL E 146 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ARG E 170 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 89 through 90 removed outlier: 3.563A pdb=" N LEU F 90 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE F 33 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS F 32 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR F 127 " --> pdb=" O ILE F 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 65 through 68 removed outlier: 4.014A pdb=" N GLY F 85 " --> pdb=" O THR F 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 123 through 124 removed outlier: 6.534A pdb=" N TYR J 16 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LEU J 57 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL J 18 " --> pdb=" O LEU J 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 73 through 74 Processing sheet with id=AA9, first strand: chain 'K' and resid 7 through 8 removed outlier: 4.325A pdb=" N VAL K 19 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ALA K 16 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA K 46 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ARG K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE K 41 " --> pdb=" O LEU K 58 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU K 58 " --> pdb=" O ILE K 41 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL K 62 " --> pdb=" O VAL K 85 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL K 85 " --> pdb=" O VAL K 62 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 78 through 79 removed outlier: 3.665A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILE P 63 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N GLY P 44 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS P 36 " --> pdb=" O GLU P 33 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG P 38 " --> pdb=" O VAL P 31 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR P 24 " --> pdb=" O VAL P 85 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL P 85 " --> pdb=" O THR P 24 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU P 26 " --> pdb=" O ILE P 83 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE P 83 " --> pdb=" O GLU P 26 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS P 28 " --> pdb=" O ASP P 81 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 89 through 90 Processing sheet with id=AB3, first strand: chain 'N' and resid 33 through 36 removed outlier: 3.750A pdb=" N ILE N 34 " --> pdb=" O ILE N 113 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ALA N 108 " --> pdb=" O PHE N 102 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE N 102 " --> pdb=" O ALA N 108 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'O' and resid 25 through 30 removed outlier: 7.117A pdb=" N ALA O 37 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ALA O 50 " --> pdb=" O ALA O 37 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL O 39 " --> pdb=" O LEU O 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.609A pdb=" N HIS R 12 " --> pdb=" O PHE R 5 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE R 5 " --> pdb=" O HIS R 12 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TYR R 2 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA R 42 " --> pdb=" O TYR R 2 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL R 4 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE R 41 " --> pdb=" O VAL R 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 19 through 22 removed outlier: 6.770A pdb=" N PHE R 93 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N HIS R 66 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'R' and resid 74 through 78 removed outlier: 4.542A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 3 through 10 removed outlier: 5.464A pdb=" N ILE S 4 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL S 107 " --> pdb=" O ILE S 4 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LYS S 6 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL S 105 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ARG S 8 " --> pdb=" O ILE S 103 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE S 103 " --> pdb=" O ARG S 8 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LYS S 98 " --> pdb=" O SER S 81 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER S 81 " --> pdb=" O LYS S 98 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR S 104 " --> pdb=" O PHE S 75 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 21 through 22 removed outlier: 4.124A pdb=" N ILE U 71 " --> pdb=" O ASP U 80 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP U 80 " --> pdb=" O ILE U 71 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS U 78 " --> pdb=" O ASN U 73 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'U' and resid 24 through 27 removed outlier: 7.083A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'U' and resid 43 through 44 Processing sheet with id=AC3, first strand: chain 'U' and resid 82 through 85 removed outlier: 4.105A pdb=" N ARG U 85 " --> pdb=" O VAL U 92 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL U 92 " --> pdb=" O ARG U 85 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'V' and resid 3 through 5 removed outlier: 6.030A pdb=" N ILE V 4 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASP V 90 " --> pdb=" O GLN V 75 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N VAL V 77 " --> pdb=" O HIS V 88 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N HIS V 88 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ARG V 79 " --> pdb=" O LEU V 86 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU V 86 " --> pdb=" O ARG V 79 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLN V 87 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG V 93 " --> pdb=" O TYR V 31 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE V 26 " --> pdb=" O LEU V 42 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU V 42 " --> pdb=" O PHE V 26 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'W' and resid 18 through 19 removed outlier: 3.826A pdb=" N GLY W 18 " --> pdb=" O ARG W 35 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU W 55 " --> pdb=" O ILE W 33 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE W 56 " --> pdb=" O GLY W 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'W' and resid 26 through 27 removed outlier: 3.718A pdb=" N VAL W 27 " --> pdb=" O GLY W 61 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY W 61 " --> pdb=" O VAL W 27 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N HIS W 42 " --> pdb=" O ILE W 76 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ILE W 78 " --> pdb=" O HIS W 42 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Z' and resid 34 through 38 586 hydrogen bonds defined for protein. 1620 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1506 hydrogen bonds 2400 hydrogen bond angles 0 basepair planarities 593 basepair parallelities 822 stacking parallelities Total time for adding SS restraints: 54.62 Time building geometry restraints manager: 14.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9924 1.33 - 1.46: 24011 1.46 - 1.58: 21784 1.58 - 1.70: 3562 1.70 - 1.82: 85 Bond restraints: 59366 Sorted by residual: bond pdb=" O5' C A1270 " pdb=" C5' C A1270 " ideal model delta sigma weight residual 1.420 1.458 -0.038 1.50e-02 4.44e+03 6.30e+00 bond pdb=" O5' C A2394 " pdb=" C5' C A2394 " ideal model delta sigma weight residual 1.420 1.450 -0.030 1.50e-02 4.44e+03 4.10e+00 bond pdb=" O5' C A2422 " pdb=" C5' C A2422 " ideal model delta sigma weight residual 1.424 1.454 -0.030 1.50e-02 4.44e+03 4.09e+00 bond pdb=" P C A1270 " pdb=" O5' C A1270 " ideal model delta sigma weight residual 1.593 1.623 -0.030 1.50e-02 4.44e+03 4.06e+00 bond pdb=" O5' U A2393 " pdb=" C5' U A2393 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.69e+00 ... (remaining 59361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 88783 2.64 - 5.29: 188 5.29 - 7.93: 16 7.93 - 10.58: 2 10.58 - 13.22: 3 Bond angle restraints: 88992 Sorted by residual: angle pdb=" C3' U A1648 " pdb=" O3' U A1648 " pdb=" P G A1649 " ideal model delta sigma weight residual 120.20 106.98 13.22 1.50e+00 4.44e-01 7.77e+01 angle pdb=" C3' G A2737 " pdb=" O3' G A2737 " pdb=" P A A2738 " ideal model delta sigma weight residual 120.20 108.07 12.13 1.50e+00 4.44e-01 6.54e+01 angle pdb=" C3' C A2422 " pdb=" O3' C A2422 " pdb=" P U A2423 " ideal model delta sigma weight residual 120.20 109.45 10.75 1.50e+00 4.44e-01 5.13e+01 angle pdb=" C3' U A2393 " pdb=" O3' U A2393 " pdb=" P C A2394 " ideal model delta sigma weight residual 120.20 111.18 9.02 1.50e+00 4.44e-01 3.61e+01 angle pdb=" C3' A A2736 " pdb=" O3' A A2736 " pdb=" P G A2737 " ideal model delta sigma weight residual 120.20 111.79 8.41 1.50e+00 4.44e-01 3.14e+01 ... (remaining 88987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 33504 35.71 - 71.42: 3932 71.42 - 107.13: 481 107.13 - 142.84: 13 142.84 - 178.55: 2 Dihedral angle restraints: 37932 sinusoidal: 32050 harmonic: 5882 Sorted by residual: dihedral pdb=" O4' C A 140 " pdb=" C1' C A 140 " pdb=" N1 C A 140 " pdb=" C2 C A 140 " ideal model delta sinusoidal sigma weight residual -128.00 40.00 -168.00 1 1.70e+01 3.46e-03 6.57e+01 dihedral pdb=" O4' C A 323 " pdb=" C1' C A 323 " pdb=" N1 C A 323 " pdb=" C2 C A 323 " ideal model delta sinusoidal sigma weight residual -128.00 10.13 -138.13 1 1.70e+01 3.46e-03 5.80e+01 dihedral pdb=" O4' A A 221 " pdb=" C1' A A 221 " pdb=" N9 A A 221 " pdb=" C4 A A 221 " ideal model delta sinusoidal sigma weight residual -106.00 -174.94 68.94 1 1.70e+01 3.46e-03 2.13e+01 ... (remaining 37929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 11213 0.096 - 0.192: 193 0.192 - 0.287: 0 0.287 - 0.383: 2 0.383 - 0.479: 7 Chirality restraints: 11415 Sorted by residual: chirality pdb=" P C A2422 " pdb=" OP1 C A2422 " pdb=" OP2 C A2422 " pdb=" O5' C A2422 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.73e+00 chirality pdb=" P C A1270 " pdb=" OP1 C A1270 " pdb=" OP2 C A1270 " pdb=" O5' C A1270 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.69e+00 chirality pdb=" P U A2423 " pdb=" OP1 U A2423 " pdb=" OP2 U A2423 " pdb=" O5' U A2423 " both_signs ideal model delta sigma weight residual True 2.41 -2.84 -0.43 2.00e-01 2.50e+01 4.55e+00 ... (remaining 11412 not shown) Planarity restraints: 4604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 259 " 0.010 2.00e-02 2.50e+03 1.76e-02 9.26e+00 pdb=" N9 G A 259 " -0.003 2.00e-02 2.50e+03 pdb=" C8 G A 259 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G A 259 " 0.007 2.00e-02 2.50e+03 pdb=" C5 G A 259 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G A 259 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G A 259 " 0.009 2.00e-02 2.50e+03 pdb=" N1 G A 259 " 0.000 2.00e-02 2.50e+03 pdb=" C2 G A 259 " -0.047 2.00e-02 2.50e+03 pdb=" N2 G A 259 " 0.034 2.00e-02 2.50e+03 pdb=" N3 G A 259 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G A 259 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 464 " -0.030 2.00e-02 2.50e+03 1.64e-02 6.02e+00 pdb=" N1 U A 464 " 0.038 2.00e-02 2.50e+03 pdb=" C2 U A 464 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U A 464 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U A 464 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U A 464 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U A 464 " -0.008 2.00e-02 2.50e+03 pdb=" C5 U A 464 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U A 464 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 239 " 0.001 2.00e-02 2.50e+03 1.52e-02 5.22e+00 pdb=" N1 C A 239 " 0.002 2.00e-02 2.50e+03 pdb=" C2 C A 239 " 0.036 2.00e-02 2.50e+03 pdb=" O2 C A 239 " -0.026 2.00e-02 2.50e+03 pdb=" N3 C A 239 " -0.000 2.00e-02 2.50e+03 pdb=" C4 C A 239 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C A 239 " -0.002 2.00e-02 2.50e+03 pdb=" C5 C A 239 " -0.007 2.00e-02 2.50e+03 pdb=" C6 C A 239 " -0.007 2.00e-02 2.50e+03 ... (remaining 4601 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 140 2.27 - 2.93: 21032 2.93 - 3.58: 89075 3.58 - 4.24: 157215 4.24 - 4.90: 212679 Nonbonded interactions: 480141 Sorted by model distance: nonbonded pdb=" O3' C A1270 " pdb=" P U A1648 " model vdw 1.610 3.400 nonbonded pdb=" O2' G B 51 " pdb=" O4' A B 52 " model vdw 1.787 3.040 nonbonded pdb=" O2' A A2635 " pdb=" OE2 GLU D 81 " model vdw 1.808 3.040 nonbonded pdb=" O2' A A1652 " pdb=" O4' G A1653 " model vdw 1.860 3.040 nonbonded pdb=" O2' U A 571 " pdb=" OP2 U A 573 " model vdw 1.881 3.040 ... (remaining 480136 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.870 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: 0.040 Extract box with map and model: 1.960 Check model and map are aligned: 0.440 Set scattering table: 0.440 Process input model: 151.460 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 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 : 0.002 0.038 59366 Z= 0.106 Angle : 0.411 13.224 88992 Z= 0.220 Chirality : 0.030 0.479 11415 Planarity : 0.003 0.053 4604 Dihedral : 22.438 178.550 34134 Min Nonbonded Distance : 1.610 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.19), residues: 2024 helix: 1.71 (0.22), residues: 626 sheet: 0.45 (0.29), residues: 345 loop : -0.93 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 125 HIS 0.004 0.000 HIS Q 13 PHE 0.020 0.001 PHE V 56 TYR 0.006 0.001 TYR S 38 ARG 0.006 0.000 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 2.940 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: 0 33 SER cc_start: 0.7288 (p) cc_final: 0.6744 (m) REVERT: 2 29 GLN cc_start: 0.9013 (tp-100) cc_final: 0.8751 (tp-100) REVERT: D 11 MET cc_start: 0.6401 (ppp) cc_final: 0.6109 (ppp) REVERT: D 174 SER cc_start: 0.8747 (m) cc_final: 0.8010 (t) REVERT: J 58 ASN cc_start: 0.8028 (m110) cc_final: 0.7743 (m110) REVERT: J 60 ASP cc_start: 0.7799 (p0) cc_final: 0.7432 (p0) REVERT: K 7 MET cc_start: 0.7538 (tpt) cc_final: 0.6613 (tpt) REVERT: L 115 GLU cc_start: 0.7990 (mp0) cc_final: 0.7726 (mp0) REVERT: N 43 GLU cc_start: 0.8046 (tp30) cc_final: 0.7845 (tp30) REVERT: N 75 ILE cc_start: 0.9438 (mm) cc_final: 0.9101 (mm) REVERT: O 24 THR cc_start: 0.7922 (p) cc_final: 0.7624 (m) REVERT: O 104 GLN cc_start: 0.7786 (tt0) cc_final: 0.7555 (tm-30) REVERT: P 1 SER cc_start: 0.8343 (t) cc_final: 0.8107 (t) REVERT: P 4 ILE cc_start: 0.8159 (mm) cc_final: 0.7897 (mm) REVERT: P 30 TRP cc_start: 0.7677 (m100) cc_final: 0.7170 (m100) REVERT: P 40 GLN cc_start: 0.6802 (tt0) cc_final: 0.6493 (tt0) REVERT: P 42 PHE cc_start: 0.8019 (t80) cc_final: 0.7578 (t80) REVERT: P 73 PHE cc_start: 0.7505 (m-80) cc_final: 0.6734 (m-80) REVERT: V 17 SER cc_start: 0.8812 (m) cc_final: 0.8088 (t) REVERT: V 44 HIS cc_start: 0.7579 (t70) cc_final: 0.6882 (t70) REVERT: W 33 ILE cc_start: 0.9209 (mm) cc_final: 0.8951 (mm) REVERT: Y 9 LYS cc_start: 0.8567 (ptpt) cc_final: 0.8116 (ptpp) REVERT: Z 31 ILE cc_start: 0.9334 (mt) cc_final: 0.9121 (mt) outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.6798 time to fit residues: 502.3568 Evaluate side-chains 291 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 3.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 0.5980 chunk 284 optimal weight: 3.9990 chunk 158 optimal weight: 40.0000 chunk 97 optimal weight: 10.0000 chunk 192 optimal weight: 30.0000 chunk 152 optimal weight: 10.0000 chunk 294 optimal weight: 30.0000 chunk 114 optimal weight: 10.0000 chunk 179 optimal weight: 40.0000 chunk 219 optimal weight: 5.9990 chunk 341 optimal weight: 10.0000 overall best weight: 6.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 GLN ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 HIS ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS U 53 GLN ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 72 ASN ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 45 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 59366 Z= 0.315 Angle : 0.641 10.409 88992 Z= 0.320 Chirality : 0.034 0.259 11415 Planarity : 0.005 0.072 4604 Dihedral : 23.225 172.574 30106 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.32 % Allowed : 12.15 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.19), residues: 2024 helix: 0.77 (0.21), residues: 647 sheet: 0.00 (0.28), residues: 366 loop : -1.16 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 60 HIS 0.008 0.002 HIS V 44 PHE 0.018 0.002 PHE V 56 TYR 0.031 0.002 TYR V 31 ARG 0.010 0.001 ARG S 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 336 time to evaluate : 3.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 22 MET cc_start: 0.8249 (mmm) cc_final: 0.7781 (mmm) REVERT: 2 29 GLN cc_start: 0.9193 (tp-100) cc_final: 0.8823 (tp-100) REVERT: F 144 LYS cc_start: 0.7554 (mttt) cc_final: 0.6967 (mmmt) REVERT: J 58 ASN cc_start: 0.8503 (m110) cc_final: 0.8235 (m110) REVERT: J 60 ASP cc_start: 0.7974 (p0) cc_final: 0.7649 (p0) REVERT: K 82 ASN cc_start: 0.8268 (t0) cc_final: 0.8033 (p0) REVERT: L 115 GLU cc_start: 0.7958 (mp0) cc_final: 0.7549 (mp0) REVERT: L 132 ARG cc_start: 0.8539 (tpt-90) cc_final: 0.8085 (tpp-160) REVERT: N 15 SER cc_start: 0.9152 (p) cc_final: 0.8934 (p) REVERT: N 24 MET cc_start: 0.8429 (mtp) cc_final: 0.7651 (mmm) REVERT: O 2 ASP cc_start: 0.7034 (m-30) cc_final: 0.6760 (t0) REVERT: O 24 THR cc_start: 0.8116 (p) cc_final: 0.7716 (t) REVERT: O 104 GLN cc_start: 0.7721 (tt0) cc_final: 0.7410 (tm-30) REVERT: P 30 TRP cc_start: 0.7872 (m100) cc_final: 0.7055 (m100) REVERT: P 40 GLN cc_start: 0.6798 (tt0) cc_final: 0.6479 (tt0) REVERT: V 17 SER cc_start: 0.8552 (m) cc_final: 0.7777 (t) REVERT: V 40 ILE cc_start: 0.8109 (tp) cc_final: 0.7816 (mp) REVERT: W 17 LEU cc_start: 0.7922 (mt) cc_final: 0.7627 (mp) REVERT: W 26 SER cc_start: 0.9491 (m) cc_final: 0.9248 (p) REVERT: W 33 ILE cc_start: 0.9191 (mm) cc_final: 0.8982 (tt) REVERT: W 73 ARG cc_start: 0.7561 (mtm180) cc_final: 0.7247 (mtm180) REVERT: Y 9 LYS cc_start: 0.8578 (ptpt) cc_final: 0.8152 (ptpp) REVERT: Y 49 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.8095 (t0) REVERT: Z 26 LEU cc_start: 0.8906 (tp) cc_final: 0.8630 (tp) outliers start: 39 outliers final: 27 residues processed: 349 average time/residue: 0.6369 time to fit residues: 378.3261 Evaluate side-chains 312 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 284 time to evaluate : 2.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 43 THR Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 76 HIS Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain K residue 23 LYS Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain Q residue 74 SER Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Z residue 24 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 284 optimal weight: 2.9990 chunk 232 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 342 optimal weight: 8.9990 chunk 369 optimal weight: 0.0980 chunk 304 optimal weight: 8.9990 chunk 339 optimal weight: 2.9990 chunk 116 optimal weight: 20.0000 chunk 274 optimal weight: 1.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN N 107 ASN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS Y 20 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 59366 Z= 0.184 Angle : 0.518 9.876 88992 Z= 0.262 Chirality : 0.030 0.214 11415 Planarity : 0.004 0.039 4604 Dihedral : 23.171 175.260 30106 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.68 % Allowed : 15.07 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.18), residues: 2024 helix: 0.48 (0.21), residues: 653 sheet: -0.08 (0.28), residues: 358 loop : -1.31 (0.18), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 60 HIS 0.005 0.001 HIS V 44 PHE 0.035 0.002 PHE 2 18 TYR 0.024 0.002 TYR 0 47 ARG 0.007 0.001 ARG L 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 330 time to evaluate : 2.979 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: 2 29 GLN cc_start: 0.9078 (tp-100) cc_final: 0.8836 (tp-100) REVERT: D 168 GLU cc_start: 0.8549 (pm20) cc_final: 0.8171 (pm20) REVERT: J 31 GLU cc_start: 0.7639 (tp30) cc_final: 0.7364 (tp30) REVERT: J 58 ASN cc_start: 0.8482 (m110) cc_final: 0.8239 (m110) REVERT: J 60 ASP cc_start: 0.7817 (p0) cc_final: 0.7459 (p0) REVERT: L 115 GLU cc_start: 0.7948 (mp0) cc_final: 0.7438 (mp0) REVERT: L 142 ILE cc_start: 0.8201 (mm) cc_final: 0.7879 (mm) REVERT: N 15 SER cc_start: 0.9112 (p) cc_final: 0.8874 (p) REVERT: N 43 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8008 (mm-30) REVERT: O 2 ASP cc_start: 0.7062 (m-30) cc_final: 0.6811 (t0) REVERT: O 24 THR cc_start: 0.7930 (p) cc_final: 0.7436 (m) REVERT: O 104 GLN cc_start: 0.7590 (tt0) cc_final: 0.7290 (tm-30) REVERT: P 30 TRP cc_start: 0.7869 (m100) cc_final: 0.7034 (m100) REVERT: P 40 GLN cc_start: 0.6831 (tt0) cc_final: 0.6547 (tt0) REVERT: R 40 MET cc_start: 0.7565 (tmm) cc_final: 0.7358 (ttt) REVERT: S 77 ASP cc_start: 0.8028 (t0) cc_final: 0.7804 (t0) REVERT: S 78 GLU cc_start: 0.8408 (tp30) cc_final: 0.8004 (tp30) REVERT: V 17 SER cc_start: 0.8695 (m) cc_final: 0.7835 (t) REVERT: V 40 ILE cc_start: 0.8136 (tp) cc_final: 0.7829 (mp) REVERT: W 17 LEU cc_start: 0.8010 (mt) cc_final: 0.7637 (mp) REVERT: W 26 SER cc_start: 0.9495 (m) cc_final: 0.9215 (p) REVERT: W 73 ARG cc_start: 0.7309 (mtm180) cc_final: 0.7005 (mtm180) REVERT: Y 5 GLU cc_start: 0.7010 (pm20) cc_final: 0.6804 (pm20) REVERT: Y 9 LYS cc_start: 0.8434 (ptpt) cc_final: 0.8053 (ptpp) REVERT: Y 49 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.7950 (t0) REVERT: Z 26 LEU cc_start: 0.8854 (tp) cc_final: 0.8551 (tp) outliers start: 45 outliers final: 28 residues processed: 350 average time/residue: 0.6377 time to fit residues: 380.6875 Evaluate side-chains 320 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 291 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 23 LYS Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain Q residue 74 SER Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Y residue 49 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 8.9990 chunk 257 optimal weight: 10.0000 chunk 177 optimal weight: 30.0000 chunk 37 optimal weight: 10.0000 chunk 163 optimal weight: 20.0000 chunk 229 optimal weight: 10.0000 chunk 343 optimal weight: 0.9980 chunk 363 optimal weight: 20.0000 chunk 179 optimal weight: 30.0000 chunk 325 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 ASN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 41 HIS Y 45 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.134 59366 Z= 0.396 Angle : 0.755 13.791 88992 Z= 0.377 Chirality : 0.039 0.442 11415 Planarity : 0.006 0.059 4604 Dihedral : 23.464 176.036 30106 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 4.65 % Allowed : 16.50 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.18), residues: 2024 helix: -0.04 (0.20), residues: 653 sheet: -0.42 (0.29), residues: 331 loop : -1.61 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 60 HIS 0.011 0.002 HIS Q 13 PHE 0.042 0.003 PHE Y 26 TYR 0.033 0.003 TYR 0 47 ARG 0.009 0.001 ARG Q 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 298 time to evaluate : 3.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 29 GLN cc_start: 0.9239 (tp-100) cc_final: 0.8988 (tp-100) REVERT: D 11 MET cc_start: 0.7105 (ptt) cc_final: 0.6750 (ttp) REVERT: F 135 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7440 (pt) REVERT: F 144 LYS cc_start: 0.7935 (mttt) cc_final: 0.7314 (mmmt) REVERT: J 60 ASP cc_start: 0.8018 (p0) cc_final: 0.7672 (p0) REVERT: K 7 MET cc_start: 0.7096 (tpt) cc_final: 0.6690 (tpt) REVERT: L 115 GLU cc_start: 0.7860 (mp0) cc_final: 0.7265 (mp0) REVERT: O 104 GLN cc_start: 0.7847 (tt0) cc_final: 0.7504 (tm-30) REVERT: P 4 ILE cc_start: 0.8647 (mm) cc_final: 0.8425 (mm) REVERT: P 30 TRP cc_start: 0.8015 (m100) cc_final: 0.7337 (m100) REVERT: P 40 GLN cc_start: 0.6869 (tt0) cc_final: 0.6616 (tt0) REVERT: Q 31 TYR cc_start: 0.9083 (t80) cc_final: 0.8729 (t80) REVERT: Q 56 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8561 (m-10) REVERT: R 26 ASP cc_start: 0.7342 (OUTLIER) cc_final: 0.6944 (p0) REVERT: R 27 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7598 (mm) REVERT: R 37 GLU cc_start: 0.7315 (pt0) cc_final: 0.7095 (pt0) REVERT: S 51 LEU cc_start: 0.9434 (tp) cc_final: 0.9202 (tt) REVERT: S 78 GLU cc_start: 0.8654 (tp30) cc_final: 0.8386 (tp30) REVERT: V 1 MET cc_start: 0.8102 (tpp) cc_final: 0.7247 (tpp) REVERT: V 57 TYR cc_start: 0.3965 (OUTLIER) cc_final: 0.3251 (m-80) REVERT: W 26 SER cc_start: 0.9534 (m) cc_final: 0.9291 (p) REVERT: W 35 ARG cc_start: 0.8931 (mtt-85) cc_final: 0.8594 (mtp85) REVERT: W 73 ARG cc_start: 0.7445 (mtm180) cc_final: 0.7039 (mtm180) REVERT: Y 9 LYS cc_start: 0.8640 (ptpt) cc_final: 0.8188 (ptpp) REVERT: Y 49 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.8089 (m-30) REVERT: Z 26 LEU cc_start: 0.8937 (tp) cc_final: 0.8730 (tp) REVERT: Z 55 LYS cc_start: 0.8634 (tptp) cc_final: 0.8429 (tptt) outliers start: 78 outliers final: 43 residues processed: 339 average time/residue: 0.6347 time to fit residues: 368.1034 Evaluate side-chains 310 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 261 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 38 LEU Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 75 TYR Chi-restraints excluded: chain J residue 76 HIS Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 56 PHE Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 57 TYR Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 79 GLU Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Z residue 24 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 20.0000 chunk 206 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 270 optimal weight: 0.9980 chunk 149 optimal weight: 20.0000 chunk 310 optimal weight: 0.9990 chunk 251 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 185 optimal weight: 10.0000 chunk 326 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 41 HIS Y 45 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 59366 Z= 0.205 Angle : 0.570 10.373 88992 Z= 0.289 Chirality : 0.032 0.249 11415 Planarity : 0.004 0.045 4604 Dihedral : 23.366 176.307 30106 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.11 % Favored : 92.84 % Rotamer: Outliers : 3.69 % Allowed : 19.71 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.18), residues: 2024 helix: 0.22 (0.21), residues: 648 sheet: -0.35 (0.29), residues: 321 loop : -1.52 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 60 HIS 0.004 0.001 HIS V 44 PHE 0.025 0.002 PHE 2 18 TYR 0.025 0.002 TYR V 31 ARG 0.007 0.001 ARG Y 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 307 time to evaluate : 2.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 30 ASP cc_start: 0.7688 (t70) cc_final: 0.7364 (t70) REVERT: 2 29 GLN cc_start: 0.9165 (tp-100) cc_final: 0.8889 (tp-100) REVERT: D 164 GLN cc_start: 0.9085 (tp-100) cc_final: 0.8737 (tm-30) REVERT: D 174 SER cc_start: 0.9373 (m) cc_final: 0.8718 (p) REVERT: F 25 MET cc_start: 0.6782 (pmm) cc_final: 0.6567 (pmm) REVERT: F 144 LYS cc_start: 0.7566 (mttt) cc_final: 0.6980 (mmmt) REVERT: J 31 GLU cc_start: 0.7631 (tp30) cc_final: 0.7407 (tp30) REVERT: J 34 ARG cc_start: 0.9417 (OUTLIER) cc_final: 0.8335 (ttm-80) REVERT: J 58 ASN cc_start: 0.8581 (m110) cc_final: 0.8273 (m110) REVERT: J 60 ASP cc_start: 0.7888 (p0) cc_final: 0.7525 (p0) REVERT: K 7 MET cc_start: 0.7042 (tpt) cc_final: 0.6653 (tpt) REVERT: L 115 GLU cc_start: 0.7828 (mp0) cc_final: 0.7487 (mp0) REVERT: N 20 MET cc_start: 0.8855 (tpt) cc_final: 0.8332 (tpt) REVERT: N 24 MET cc_start: 0.8428 (mtp) cc_final: 0.8227 (ptp) REVERT: O 24 THR cc_start: 0.7870 (p) cc_final: 0.7230 (m) REVERT: O 76 LYS cc_start: 0.9129 (mmmm) cc_final: 0.8883 (tptp) REVERT: O 104 GLN cc_start: 0.7777 (tt0) cc_final: 0.7442 (tm-30) REVERT: P 4 ILE cc_start: 0.8602 (mm) cc_final: 0.8350 (mm) REVERT: P 30 TRP cc_start: 0.8058 (m100) cc_final: 0.7367 (m100) REVERT: Q 31 TYR cc_start: 0.9039 (t80) cc_final: 0.8668 (t80) REVERT: R 26 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.6925 (p0) REVERT: R 27 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7654 (mm) REVERT: R 40 MET cc_start: 0.7825 (tmm) cc_final: 0.7320 (ttt) REVERT: R 46 GLU cc_start: 0.8504 (pm20) cc_final: 0.8175 (pm20) REVERT: V 1 MET cc_start: 0.8019 (tpp) cc_final: 0.7490 (tpp) REVERT: W 26 SER cc_start: 0.9507 (m) cc_final: 0.9237 (p) REVERT: W 73 ARG cc_start: 0.7325 (mtm180) cc_final: 0.6895 (mtm180) REVERT: Y 49 ASP cc_start: 0.8461 (m-30) cc_final: 0.8043 (m-30) REVERT: Z 26 LEU cc_start: 0.8929 (tp) cc_final: 0.8688 (tp) outliers start: 62 outliers final: 33 residues processed: 341 average time/residue: 0.6556 time to fit residues: 382.6760 Evaluate side-chains 315 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 279 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 33 SER Chi-restraints excluded: chain 0 residue 38 LEU Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 34 ARG Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 75 TYR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain O residue 4 LYS Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain V residue 29 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Y residue 50 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 10.0000 chunk 327 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 chunk 213 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 363 optimal weight: 20.0000 chunk 301 optimal weight: 0.0000 chunk 168 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 190 optimal weight: 0.8980 overall best weight: 5.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 59366 Z= 0.304 Angle : 0.637 10.305 88992 Z= 0.322 Chirality : 0.035 0.460 11415 Planarity : 0.005 0.047 4604 Dihedral : 23.392 177.286 30106 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 4.65 % Allowed : 20.43 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.18), residues: 2024 helix: 0.06 (0.21), residues: 658 sheet: -0.55 (0.29), residues: 329 loop : -1.67 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 60 HIS 0.005 0.001 HIS V 44 PHE 0.031 0.002 PHE R 53 TYR 0.021 0.002 TYR Q 31 ARG 0.008 0.001 ARG V 93 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 282 time to evaluate : 3.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 30 ASP cc_start: 0.7773 (t70) cc_final: 0.7482 (t70) REVERT: 2 29 GLN cc_start: 0.9177 (tp-100) cc_final: 0.8927 (tp-100) REVERT: D 174 SER cc_start: 0.9415 (m) cc_final: 0.8781 (p) REVERT: F 25 MET cc_start: 0.7031 (pmm) cc_final: 0.6820 (pmm) REVERT: F 144 LYS cc_start: 0.7616 (mttt) cc_final: 0.6977 (mmmt) REVERT: J 31 GLU cc_start: 0.7628 (tp30) cc_final: 0.7356 (tp30) REVERT: J 34 ARG cc_start: 0.9454 (OUTLIER) cc_final: 0.8352 (ttm-80) REVERT: J 60 ASP cc_start: 0.7931 (p0) cc_final: 0.7581 (p0) REVERT: K 7 MET cc_start: 0.6982 (tpt) cc_final: 0.6591 (tpt) REVERT: L 115 GLU cc_start: 0.7782 (mp0) cc_final: 0.7429 (mp0) REVERT: O 76 LYS cc_start: 0.9142 (mmmm) cc_final: 0.8914 (tptp) REVERT: O 104 GLN cc_start: 0.7817 (tt0) cc_final: 0.7467 (tm-30) REVERT: P 4 ILE cc_start: 0.8667 (mm) cc_final: 0.8442 (mm) REVERT: R 26 ASP cc_start: 0.7277 (OUTLIER) cc_final: 0.6944 (p0) REVERT: R 27 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7816 (mm) REVERT: S 31 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8422 (pt0) REVERT: U 86 PHE cc_start: 0.7279 (OUTLIER) cc_final: 0.6427 (m-80) REVERT: V 1 MET cc_start: 0.8056 (tpp) cc_final: 0.7299 (tmm) REVERT: W 26 SER cc_start: 0.9480 (m) cc_final: 0.9226 (p) REVERT: W 35 ARG cc_start: 0.8907 (mtt-85) cc_final: 0.8658 (mtp85) REVERT: W 73 ARG cc_start: 0.7368 (mtm180) cc_final: 0.7014 (mtm180) REVERT: Y 2 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8056 (mtmm) REVERT: Y 49 ASP cc_start: 0.8432 (m-30) cc_final: 0.8078 (m-30) outliers start: 78 outliers final: 50 residues processed: 326 average time/residue: 0.6492 time to fit residues: 365.1256 Evaluate side-chains 317 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 261 time to evaluate : 3.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 0 residue 33 SER Chi-restraints excluded: chain 0 residue 38 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 34 ARG Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 75 TYR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 23 LYS Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 79 GLU Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Z residue 24 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 0.0670 chunk 41 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 265 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 306 optimal weight: 20.0000 chunk 203 optimal weight: 6.9990 chunk 362 optimal weight: 9.9990 chunk 226 optimal weight: 30.0000 chunk 220 optimal weight: 0.6980 chunk 167 optimal weight: 10.0000 overall best weight: 2.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN Q 51 GLN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 59366 Z= 0.181 Angle : 0.553 14.794 88992 Z= 0.281 Chirality : 0.031 0.273 11415 Planarity : 0.004 0.048 4604 Dihedral : 23.335 177.275 30106 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 4.11 % Allowed : 21.86 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.18), residues: 2024 helix: 0.15 (0.21), residues: 659 sheet: -0.48 (0.29), residues: 324 loop : -1.63 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 60 HIS 0.003 0.001 HIS J 47 PHE 0.031 0.002 PHE F 121 TYR 0.023 0.002 TYR V 31 ARG 0.007 0.001 ARG V 93 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 295 time to evaluate : 2.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 30 ASP cc_start: 0.7674 (t70) cc_final: 0.7301 (t70) REVERT: 2 29 GLN cc_start: 0.9148 (tp-100) cc_final: 0.8895 (tp-100) REVERT: D 164 GLN cc_start: 0.9076 (tp-100) cc_final: 0.8489 (tp40) REVERT: D 174 SER cc_start: 0.9385 (m) cc_final: 0.8742 (p) REVERT: F 127 TYR cc_start: 0.3402 (t80) cc_final: 0.3183 (t80) REVERT: J 34 ARG cc_start: 0.9393 (OUTLIER) cc_final: 0.8258 (ttm-80) REVERT: J 58 ASN cc_start: 0.8552 (m110) cc_final: 0.8286 (m110) REVERT: J 60 ASP cc_start: 0.7848 (p0) cc_final: 0.7514 (p0) REVERT: K 7 MET cc_start: 0.6762 (tpt) cc_final: 0.6493 (tpt) REVERT: L 115 GLU cc_start: 0.7775 (mp0) cc_final: 0.7257 (mp0) REVERT: O 48 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8231 (mm) REVERT: O 76 LYS cc_start: 0.9076 (mmmm) cc_final: 0.8859 (tptp) REVERT: O 104 GLN cc_start: 0.7759 (tt0) cc_final: 0.7427 (tm-30) REVERT: R 26 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.7004 (p0) REVERT: R 27 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7714 (mm) REVERT: U 86 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6407 (m-80) REVERT: V 1 MET cc_start: 0.8152 (tpp) cc_final: 0.7815 (tmm) REVERT: W 26 SER cc_start: 0.9482 (m) cc_final: 0.9140 (p) REVERT: W 73 ARG cc_start: 0.7384 (mtm180) cc_final: 0.6996 (mtm180) REVERT: Y 9 LYS cc_start: 0.8410 (ptpt) cc_final: 0.8073 (ptpp) REVERT: Y 49 ASP cc_start: 0.8511 (m-30) cc_final: 0.7987 (m-30) outliers start: 69 outliers final: 48 residues processed: 334 average time/residue: 0.6710 time to fit residues: 384.5856 Evaluate side-chains 319 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 266 time to evaluate : 3.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 0 residue 33 SER Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 34 ARG Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 75 TYR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 22 ASP Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Z residue 24 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 30.0000 chunk 144 optimal weight: 40.0000 chunk 216 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 230 optimal weight: 8.9990 chunk 246 optimal weight: 10.0000 chunk 179 optimal weight: 40.0000 chunk 33 optimal weight: 20.0000 chunk 284 optimal weight: 10.0000 overall best weight: 9.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN P 114 ASN ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 59366 Z= 0.443 Angle : 0.779 10.755 88992 Z= 0.388 Chirality : 0.041 0.315 11415 Planarity : 0.006 0.059 4604 Dihedral : 23.576 177.857 30106 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 21.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.03 % Favored : 89.92 % Rotamer: Outliers : 4.71 % Allowed : 21.74 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.18), residues: 2024 helix: -0.13 (0.20), residues: 643 sheet: -0.80 (0.29), residues: 331 loop : -1.90 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP P 30 HIS 0.011 0.002 HIS N 31 PHE 0.027 0.002 PHE R 93 TYR 0.032 0.003 TYR J 53 ARG 0.008 0.001 ARG Q 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 260 time to evaluate : 3.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 29 GLN cc_start: 0.9265 (tp-100) cc_final: 0.9040 (tp-100) REVERT: D 164 GLN cc_start: 0.8920 (tp-100) cc_final: 0.8679 (tm-30) REVERT: F 25 MET cc_start: 0.7095 (pmm) cc_final: 0.6870 (pmm) REVERT: J 34 ARG cc_start: 0.9377 (OUTLIER) cc_final: 0.8287 (ttm-80) REVERT: J 60 ASP cc_start: 0.8186 (p0) cc_final: 0.7843 (p0) REVERT: N 24 MET cc_start: 0.8602 (mtp) cc_final: 0.8182 (mtm) REVERT: O 48 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8100 (mm) REVERT: O 104 GLN cc_start: 0.7818 (tt0) cc_final: 0.7452 (tm-30) REVERT: P 63 ILE cc_start: 0.8658 (pt) cc_final: 0.8442 (tp) REVERT: R 26 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.7049 (p0) REVERT: R 27 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7884 (mm) REVERT: R 55 ASP cc_start: 0.8723 (p0) cc_final: 0.8467 (p0) REVERT: S 31 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8492 (pt0) REVERT: V 1 MET cc_start: 0.8219 (tpp) cc_final: 0.7887 (tmm) REVERT: W 26 SER cc_start: 0.9532 (m) cc_final: 0.9321 (p) REVERT: W 35 ARG cc_start: 0.9008 (mtt-85) cc_final: 0.8469 (mtp85) REVERT: W 73 ARG cc_start: 0.7412 (mtm180) cc_final: 0.7066 (mtm180) REVERT: Y 2 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8287 (mtmm) REVERT: Y 49 ASP cc_start: 0.8651 (m-30) cc_final: 0.8152 (m-30) outliers start: 79 outliers final: 58 residues processed: 308 average time/residue: 0.6427 time to fit residues: 338.5282 Evaluate side-chains 317 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 253 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 0 residue 33 SER Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 34 ARG Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 75 TYR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 23 LYS Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 22 ASP Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 79 GLU Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 24 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 3.9990 chunk 347 optimal weight: 0.6980 chunk 316 optimal weight: 2.9990 chunk 337 optimal weight: 6.9990 chunk 203 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 265 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 305 optimal weight: 20.0000 chunk 319 optimal weight: 5.9990 chunk 336 optimal weight: 1.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN J 138 GLN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 59366 Z= 0.198 Angle : 0.595 16.725 88992 Z= 0.301 Chirality : 0.033 0.252 11415 Planarity : 0.004 0.053 4604 Dihedral : 23.461 177.535 30106 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.16 % Favored : 92.79 % Rotamer: Outliers : 3.87 % Allowed : 23.05 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.18), residues: 2024 helix: 0.00 (0.21), residues: 655 sheet: -0.62 (0.29), residues: 317 loop : -1.80 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 60 HIS 0.007 0.001 HIS N 31 PHE 0.025 0.002 PHE 2 18 TYR 0.027 0.002 TYR V 31 ARG 0.008 0.001 ARG Y 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 283 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 29 GLN cc_start: 0.9166 (tp-100) cc_final: 0.8931 (tp-100) REVERT: D 164 GLN cc_start: 0.8951 (tp-100) cc_final: 0.8657 (tm-30) REVERT: D 174 SER cc_start: 0.9425 (m) cc_final: 0.8762 (p) REVERT: F 25 MET cc_start: 0.7156 (pmm) cc_final: 0.6948 (pmm) REVERT: J 34 ARG cc_start: 0.9370 (OUTLIER) cc_final: 0.8201 (ttm-80) REVERT: J 58 ASN cc_start: 0.8596 (m110) cc_final: 0.8326 (m110) REVERT: J 60 ASP cc_start: 0.7961 (p0) cc_final: 0.7630 (p0) REVERT: L 115 GLU cc_start: 0.8021 (mp0) cc_final: 0.7161 (mp0) REVERT: N 24 MET cc_start: 0.8460 (mtp) cc_final: 0.7757 (mmm) REVERT: O 48 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8236 (mm) REVERT: O 76 LYS cc_start: 0.9129 (mmmm) cc_final: 0.8884 (tptp) REVERT: O 104 GLN cc_start: 0.7798 (tt0) cc_final: 0.7471 (tm-30) REVERT: R 26 ASP cc_start: 0.7178 (OUTLIER) cc_final: 0.6887 (p0) REVERT: R 27 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7753 (mm) REVERT: R 55 ASP cc_start: 0.8432 (p0) cc_final: 0.8024 (p0) REVERT: V 1 MET cc_start: 0.8172 (tpp) cc_final: 0.7838 (tmm) REVERT: W 26 SER cc_start: 0.9494 (m) cc_final: 0.9252 (p) REVERT: W 73 ARG cc_start: 0.7393 (mtm180) cc_final: 0.7136 (mtm180) REVERT: Y 2 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7906 (mtmm) REVERT: Y 49 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.7904 (m-30) outliers start: 65 outliers final: 50 residues processed: 319 average time/residue: 0.6735 time to fit residues: 367.1897 Evaluate side-chains 325 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 269 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 0 residue 33 SER Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 34 ARG Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 75 TYR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 23 LYS Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 22 ASP Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 24 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 40.0000 chunk 357 optimal weight: 8.9990 chunk 217 optimal weight: 4.9990 chunk 169 optimal weight: 20.0000 chunk 248 optimal weight: 3.9990 chunk 374 optimal weight: 9.9990 chunk 344 optimal weight: 10.0000 chunk 298 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 230 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 59366 Z= 0.370 Angle : 0.702 11.386 88992 Z= 0.353 Chirality : 0.037 0.282 11415 Planarity : 0.005 0.132 4604 Dihedral : 23.541 178.107 30106 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.29 % Favored : 90.66 % Rotamer: Outliers : 4.05 % Allowed : 22.10 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.18), residues: 2024 helix: -0.07 (0.21), residues: 647 sheet: -0.83 (0.28), residues: 344 loop : -1.92 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 60 HIS 0.006 0.001 HIS J 40 PHE 0.024 0.002 PHE W 41 TYR 0.031 0.002 TYR J 53 ARG 0.017 0.001 ARG F 132 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 261 time to evaluate : 3.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 29 GLN cc_start: 0.9226 (tp-100) cc_final: 0.9001 (tp-100) REVERT: F 25 MET cc_start: 0.7195 (pmm) cc_final: 0.6966 (pmm) REVERT: F 135 ILE cc_start: 0.7838 (mm) cc_final: 0.7618 (mp) REVERT: F 177 ARG cc_start: 0.6203 (tpp80) cc_final: 0.5908 (tpp80) REVERT: J 34 ARG cc_start: 0.9411 (OUTLIER) cc_final: 0.8280 (ttm-80) REVERT: J 60 ASP cc_start: 0.8146 (p0) cc_final: 0.7801 (p0) REVERT: N 24 MET cc_start: 0.8522 (mtp) cc_final: 0.7869 (mmm) REVERT: O 48 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8089 (mm) REVERT: O 104 GLN cc_start: 0.7830 (tt0) cc_final: 0.7476 (tm-30) REVERT: P 63 ILE cc_start: 0.8636 (pt) cc_final: 0.8429 (tp) REVERT: R 26 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.7064 (p0) REVERT: R 27 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7856 (mm) REVERT: R 55 ASP cc_start: 0.8652 (p0) cc_final: 0.8281 (p0) REVERT: V 1 MET cc_start: 0.8259 (tpp) cc_final: 0.7824 (tmm) REVERT: W 35 ARG cc_start: 0.8982 (mtt-85) cc_final: 0.8687 (mtp85) REVERT: W 73 ARG cc_start: 0.7452 (mtm180) cc_final: 0.7203 (mtm180) REVERT: Y 2 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8174 (mtmm) REVERT: Y 9 LYS cc_start: 0.8662 (ptpt) cc_final: 0.8261 (ptpp) REVERT: Y 49 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8033 (m-30) outliers start: 68 outliers final: 57 residues processed: 300 average time/residue: 0.6563 time to fit residues: 336.4237 Evaluate side-chains 313 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 250 time to evaluate : 3.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 0 residue 33 SER Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 34 ARG Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 75 TYR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 22 ASP Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 24 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 9.9990 chunk 317 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 275 optimal weight: 9.9990 chunk 44 optimal weight: 30.0000 chunk 82 optimal weight: 10.0000 chunk 298 optimal weight: 0.8980 chunk 125 optimal weight: 10.0000 chunk 306 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 overall best weight: 7.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.070342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.049525 restraints weight = 312752.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.051034 restraints weight = 109793.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.051914 restraints weight = 65823.980| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.5467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 59366 Z= 0.352 Angle : 0.706 16.962 88992 Z= 0.357 Chirality : 0.038 0.283 11415 Planarity : 0.005 0.062 4604 Dihedral : 23.639 178.212 30106 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.99 % Favored : 90.96 % Rotamer: Outliers : 4.23 % Allowed : 22.04 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.18), residues: 2024 helix: -0.23 (0.20), residues: 644 sheet: -0.98 (0.29), residues: 332 loop : -2.01 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 96 HIS 0.005 0.001 HIS V 80 PHE 0.044 0.002 PHE R 53 TYR 0.030 0.002 TYR J 53 ARG 0.011 0.001 ARG F 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8409.01 seconds wall clock time: 208 minutes 48.66 seconds (12528.66 seconds total)