Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 09:21:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c94_16501/10_2023/8c94_16501.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c94_16501/10_2023/8c94_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_16501/10_2023/8c94_16501.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c94_16501/10_2023/8c94_16501.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c94_16501/10_2023/8c94_16501.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c94_16501/10_2023/8c94_16501.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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 Residue "R PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 20.74, per 1000 atoms: 0.38 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 24.01 Conformation dependent library (CDL) restraints added in 2.0 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: 20.02 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: 46.03 Time building geometry restraints manager: 25.72 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: 98.81 - 105.84: 9461 105.84 - 112.87: 34641 112.87 - 119.91: 20849 119.91 - 126.94: 19490 126.94 - 133.98: 4551 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: 30632 35.71 - 71.42: 798 71.42 - 107.13: 77 107.13 - 142.84: 13 142.84 - 178.55: 2 Dihedral angle restraints: 31522 sinusoidal: 25640 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 31519 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 2.440 nonbonded pdb=" O2' A A2635 " pdb=" OE2 GLU D 81 " model vdw 1.808 2.440 nonbonded pdb=" O2' A A1652 " pdb=" O4' G A1653 " model vdw 1.860 2.440 nonbonded pdb=" O2' U A 571 " pdb=" OP2 U A 573 " model vdw 1.881 2.440 ... (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 ========== 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.690 Check model and map are aligned: 0.610 Set scattering table: 0.380 Process input model: 151.130 Find NCS groups from input model: 0.960 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:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 164.470 ------------------------------------------------------------------------------- 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 : 13.064 178.550 27724 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 444 time to evaluate : 2.346 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 outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.5422 time to fit residues: 398.9438 Evaluate side-chains 281 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 2.397 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5148 ------------------------------------------------------------------------------- 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: 0.9980 chunk 284 optimal weight: 20.0000 chunk 158 optimal weight: 40.0000 chunk 97 optimal weight: 20.0000 chunk 192 optimal weight: 20.0000 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: 8.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- 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** N 107 ASN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 72 ASN Y 20 ASN Y 27 ASN Y 45 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.133 59366 Z= 0.383 Angle : 0.740 10.709 88992 Z= 0.370 Chirality : 0.037 0.268 11415 Planarity : 0.006 0.093 4604 Dihedral : 14.005 174.323 23696 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 3.22 % Allowed : 12.92 % Favored : 83.86 % 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: -0.91 (0.18), residues: 2024 helix: 0.36 (0.20), residues: 642 sheet: -0.20 (0.27), residues: 375 loop : -1.40 (0.19), residues: 1007 *********************** 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 366 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 312 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 32 residues processed: 337 average time/residue: 0.5209 time to fit residues: 299.8705 Evaluate side-chains 292 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 260 time to evaluate : 2.369 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.3863 time to fit residues: 26.0943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 284 optimal weight: 10.0000 chunk 232 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 342 optimal weight: 6.9990 chunk 369 optimal weight: 4.9990 chunk 304 optimal weight: 20.0000 chunk 339 optimal weight: 6.9990 chunk 116 optimal weight: 20.0000 chunk 274 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 N 107 ASN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN O 100 HIS Q 55 GLN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 59366 Z= 0.262 Angle : 0.574 10.530 88992 Z= 0.291 Chirality : 0.033 0.327 11415 Planarity : 0.004 0.046 4604 Dihedral : 13.854 175.848 23696 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.36 % Favored : 92.59 % Rotamer: Outliers : 2.26 % Allowed : 16.32 % Favored : 81.42 % 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: -0.94 (0.18), residues: 2024 helix: 0.42 (0.21), residues: 639 sheet: -0.17 (0.28), residues: 346 loop : -1.46 (0.18), residues: 1039 *********************** 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 344 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 306 time to evaluate : 2.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 15 residues processed: 326 average time/residue: 0.5175 time to fit residues: 291.3981 Evaluate side-chains 282 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 267 time to evaluate : 2.386 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.4317 time to fit residues: 14.4519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 6.9990 chunk 257 optimal weight: 0.0070 chunk 177 optimal weight: 30.0000 chunk 37 optimal weight: 10.0000 chunk 163 optimal weight: 20.0000 chunk 229 optimal weight: 5.9990 chunk 343 optimal weight: 4.9990 chunk 363 optimal weight: 20.0000 chunk 179 optimal weight: 30.0000 chunk 325 optimal weight: 0.1980 chunk 97 optimal weight: 20.0000 overall best weight: 3.6404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 ASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN N 107 ASN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 HIS P 114 ASN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 ASN U 65 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 59366 Z= 0.200 Angle : 0.536 10.298 88992 Z= 0.273 Chirality : 0.031 0.280 11415 Planarity : 0.004 0.050 4604 Dihedral : 13.828 176.406 23696 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.81 % Favored : 92.14 % Rotamer: Outliers : 2.68 % Allowed : 18.28 % Favored : 79.04 % 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: -0.88 (0.18), residues: 2024 helix: 0.51 (0.21), residues: 639 sheet: -0.11 (0.30), residues: 324 loop : -1.46 (0.18), residues: 1061 *********************** 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 340 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 295 time to evaluate : 2.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 18 residues processed: 319 average time/residue: 0.5024 time to fit residues: 277.1786 Evaluate side-chains 288 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 270 time to evaluate : 2.408 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3876 time to fit residues: 15.7511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 0.7980 chunk 206 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 270 optimal weight: 0.0060 chunk 149 optimal weight: 30.0000 chunk 310 optimal weight: 2.9990 chunk 251 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 185 optimal weight: 20.0000 chunk 326 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 overall best weight: 2.4800 ------------------------------------------------------------------------------- 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 N 107 ASN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 59366 Z= 0.153 Angle : 0.500 10.472 88992 Z= 0.254 Chirality : 0.029 0.257 11415 Planarity : 0.004 0.040 4604 Dihedral : 13.720 176.915 23696 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.82 % Favored : 93.13 % Rotamer: Outliers : 2.08 % Allowed : 20.01 % Favored : 77.90 % 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: -0.76 (0.19), residues: 2024 helix: 0.61 (0.21), residues: 645 sheet: -0.08 (0.30), residues: 321 loop : -1.37 (0.18), residues: 1058 *********************** 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 337 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 302 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 16 residues processed: 320 average time/residue: 0.5146 time to fit residues: 287.0918 Evaluate side-chains 297 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 281 time to evaluate : 2.385 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3881 time to fit residues: 14.5013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 71 optimal weight: 20.0000 chunk 213 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 363 optimal weight: 30.0000 chunk 301 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- 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** S 60 HIS ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 5 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 59366 Z= 0.371 Angle : 0.699 9.880 88992 Z= 0.351 Chirality : 0.037 0.461 11415 Planarity : 0.005 0.048 4604 Dihedral : 14.410 176.975 23696 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 23.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.04 % Favored : 90.91 % Rotamer: Outliers : 2.62 % Allowed : 21.50 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.21 (0.18), residues: 2024 helix: 0.21 (0.20), residues: 646 sheet: -0.35 (0.30), residues: 330 loop : -1.64 (0.18), residues: 1048 *********************** 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 328 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 284 time to evaluate : 2.411 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 28 residues processed: 303 average time/residue: 0.5216 time to fit residues: 271.8889 Evaluate side-chains 280 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 252 time to evaluate : 2.427 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.4013 time to fit residues: 23.8474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 265 optimal weight: 0.9990 chunk 205 optimal weight: 7.9990 chunk 306 optimal weight: 5.9990 chunk 203 optimal weight: 4.9990 chunk 362 optimal weight: 5.9990 chunk 226 optimal weight: 6.9990 chunk 220 optimal weight: 20.0000 chunk 167 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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** P 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 59366 Z= 0.252 Angle : 0.594 10.238 88992 Z= 0.302 Chirality : 0.034 0.360 11415 Planarity : 0.004 0.039 4604 Dihedral : 14.242 177.221 23696 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.25 % Favored : 91.70 % Rotamer: Outliers : 1.25 % Allowed : 23.94 % Favored : 74.81 % 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: -1.12 (0.18), residues: 2024 helix: 0.39 (0.21), residues: 644 sheet: -0.36 (0.30), residues: 333 loop : -1.63 (0.18), residues: 1047 *********************** 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 306 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 285 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 6 residues processed: 294 average time/residue: 0.5321 time to fit residues: 267.4465 Evaluate side-chains 266 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 260 time to evaluate : 2.430 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4112 time to fit residues: 7.2192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 6.9990 chunk 144 optimal weight: 40.0000 chunk 216 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 230 optimal weight: 3.9990 chunk 246 optimal weight: 10.0000 chunk 179 optimal weight: 30.0000 chunk 33 optimal weight: 20.0000 chunk 284 optimal weight: 9.9990 overall best weight: 7.3992 ------------------------------------------------------------------------------- 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 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.154 59366 Z= 0.369 Angle : 0.704 11.970 88992 Z= 0.354 Chirality : 0.038 0.363 11415 Planarity : 0.005 0.047 4604 Dihedral : 14.698 177.868 23696 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 24.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.78 % Favored : 90.17 % Rotamer: Outliers : 2.14 % Allowed : 22.99 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.04 (0.20), residues: 653 sheet: -0.64 (0.30), residues: 337 loop : -1.85 (0.18), residues: 1034 *********************** 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 304 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 268 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 23 residues processed: 286 average time/residue: 0.5366 time to fit residues: 262.5494 Evaluate side-chains 276 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 253 time to evaluate : 2.370 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.4043 time to fit residues: 20.0286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 4.9990 chunk 347 optimal weight: 8.9990 chunk 316 optimal weight: 2.9990 chunk 337 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 265 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 305 optimal weight: 4.9990 chunk 319 optimal weight: 0.9990 chunk 336 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** D 173 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS J 138 GLN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 59366 Z= 0.191 Angle : 0.567 10.421 88992 Z= 0.289 Chirality : 0.032 0.270 11415 Planarity : 0.004 0.041 4604 Dihedral : 14.358 177.736 23696 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.81 % Favored : 92.14 % Rotamer: Outliers : 0.60 % Allowed : 24.24 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.18), residues: 2024 helix: 0.32 (0.21), residues: 651 sheet: -0.61 (0.29), residues: 335 loop : -1.77 (0.18), residues: 1038 *********************** 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 301 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 291 time to evaluate : 2.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 293 average time/residue: 0.5259 time to fit residues: 265.6513 Evaluate side-chains 272 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 269 time to evaluate : 2.401 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4173 time to fit residues: 4.8133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 20.0000 chunk 357 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 169 optimal weight: 20.0000 chunk 248 optimal weight: 6.9990 chunk 374 optimal weight: 6.9990 chunk 344 optimal weight: 3.9990 chunk 298 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 230 optimal weight: 40.0000 chunk 182 optimal weight: 10.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- 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** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 59366 Z= 0.357 Angle : 0.682 10.172 88992 Z= 0.343 Chirality : 0.037 0.271 11415 Planarity : 0.005 0.042 4604 Dihedral : 14.674 178.222 23696 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 23.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.03 % Favored : 89.87 % Rotamer: Outliers : 1.37 % Allowed : 24.48 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.49 (0.18), residues: 2024 helix: 0.12 (0.21), residues: 655 sheet: -0.70 (0.29), residues: 337 loop : -1.85 (0.18), residues: 1032 ********************** 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 282 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 259 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 268 average time/residue: 0.5277 time to fit residues: 243.5966 Evaluate side-chains 265 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 253 time to evaluate : 2.406 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4237 time to fit residues: 11.9910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 50.0000 chunk 317 optimal weight: 0.4980 chunk 91 optimal weight: 10.0000 chunk 275 optimal weight: 20.0000 chunk 44 optimal weight: 30.0000 chunk 82 optimal weight: 10.0000 chunk 298 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 306 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 overall best weight: 7.4992 ------------------------------------------------------------------------------- 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** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN ** O 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 = 0.3620 r_free = 0.3620 target = 0.070160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.049487 restraints weight = 316734.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.050969 restraints weight = 111348.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.051846 restraints weight = 66935.598| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 59366 Z= 0.355 Angle : 0.695 11.940 88992 Z= 0.352 Chirality : 0.038 0.283 11415 Planarity : 0.005 0.044 4604 Dihedral : 14.931 178.008 23696 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 24.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.18 % Favored : 89.67 % Rotamer: Outliers : 0.60 % Allowed : 25.19 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.71 (0.18), residues: 2024 helix: -0.06 (0.20), residues: 654 sheet: -0.89 (0.29), residues: 339 loop : -1.96 (0.18), residues: 1031 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6608.71 seconds wall clock time: 121 minutes 36.36 seconds (7296.36 seconds total)