Starting phenix.real_space_refine on Fri Feb 16 15:54:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8z_16496/02_2024/8c8z_16496.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8z_16496/02_2024/8c8z_16496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8z_16496/02_2024/8c8z_16496.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8z_16496/02_2024/8c8z_16496.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8z_16496/02_2024/8c8z_16496.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8z_16496/02_2024/8c8z_16496.pdb" } resolution = 3.12 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= 0.007 sd= 0.120 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 2324 5.49 5 S 51 5.16 5 C 33610 2.51 5 N 12671 2.21 5 O 19334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "V PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 67990 Number of models: 1 Model: "" Number of chains: 24 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: "A" Number of atoms: 47374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2205, 47374 Classifications: {'RNA': 2205} Modifications used: {'rna2p_pur': 213, 'rna2p_pyr': 116, 'rna3p_pur': 1073, 'rna3p_pyr': 803} Link IDs: {'rna2p': 329, 'rna3p': 1875} Chain breaks: 7 Chain: "D" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1379 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain breaks: 1 Chain: "E" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1537 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 192} Chain breaks: 1 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: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 850 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} 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: "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: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 804 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain breaks: 1 Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} 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: "X" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 598 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain breaks: 1 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: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "2" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 322 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} 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: "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: "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: "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} Chain: "H" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 384 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "W" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 522 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 67} 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 Time building chain proxies: 31.56, per 1000 atoms: 0.46 Number of scatterers: 67990 At special positions: 0 Unit cell: (183.75, 236.25, 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 51 16.00 P 2324 15.00 O 19334 8.00 N 12671 7.00 C 33610 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: 31.71 Conformation dependent library (CDL) restraints added in 2.9 seconds 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4248 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 32 sheets defined 33.6% alpha, 19.2% beta 777 base pairs and 1132 stacking pairs defined. Time for finding SS restraints: 27.25 Creating SS restraints... Processing helix chain 'V' and resid 13 through 23 Processing helix chain 'V' and resid 44 through 52 Processing helix chain 'V' and resid 53 through 59 removed outlier: 3.645A pdb=" N PHE V 56 " --> pdb=" O LYS V 53 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR V 57 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 61 through 72 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.933A pdb=" N LEU D 100 " --> pdb=" O SER D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 40 Processing helix chain 'E' and resid 97 through 116 Processing helix chain 'E' and resid 130 through 142 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: 3.525A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 58 through 62 removed outlier: 3.854A 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 109 removed outlier: 4.054A pdb=" N VAL J 100 " --> pdb=" O ARG J 96 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 121 removed outlier: 3.640A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) 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 removed outlier: 3.822A pdb=" N ILE K 116 " --> pdb=" O PHE K 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 56 removed outlier: 4.062A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.722A 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 Processing helix chain 'N' and resid 73 through 79 Processing helix chain 'N' and resid 82 through 88 Processing helix chain 'P' and resid 2 through 10 Processing helix chain 'P' and resid 52 through 55 Processing helix chain 'P' and resid 96 through 101 removed outlier: 3.821A pdb=" N GLU P 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 108 removed outlier: 4.057A pdb=" N ARG P 108 " --> pdb=" O LYS P 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 19 Processing helix chain 'Q' and resid 25 through 30 Processing helix chain 'Q' and resid 30 through 72 removed outlier: 4.116A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 86 Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 101 through 117 Processing helix chain 'S' and resid 13 through 22 removed outlier: 3.972A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 Processing helix chain 'S' and resid 41 through 61 Processing helix chain 'T' and resid 3 through 10 Processing helix chain 'T' and resid 17 through 28 Processing helix chain 'T' and resid 39 through 52 Processing helix chain 'X' and resid 52 through 62 Processing helix chain 'X' and resid 62 through 73 removed outlier: 3.648A pdb=" N ARG X 73 " --> pdb=" O GLU X 69 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 7 removed outlier: 3.642A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 34 removed outlier: 3.871A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ARG Y 29 " --> pdb=" O GLN Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 44 removed outlier: 4.161A pdb=" N LEU Y 42 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 48 through 56 Processing helix chain '0' and resid 8 through 17 Processing helix chain '0' and resid 18 through 20 No H-bonds generated for 'chain '0' and resid 18 through 20' Processing helix chain '2' and resid 8 through 17 Processing helix chain '2' and resid 17 through 23 Processing helix chain '2' and resid 24 through 38 Processing helix chain 'O' and resid 3 through 22 removed outlier: 4.083A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN O 19 " --> pdb=" O ARG O 15 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU O 21 " --> pdb=" O LYS O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 removed outlier: 3.561A pdb=" N ALA O 59 " --> pdb=" O GLU O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 113 Processing helix chain 'F' and resid 2 through 20 removed outlier: 4.149A pdb=" N TYR F 6 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 27 removed outlier: 4.195A pdb=" N VAL F 27 " --> pdb=" O VAL F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 44 removed outlier: 4.348A pdb=" N ILE F 43 " --> pdb=" O GLY F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 60 Processing helix chain 'F' and resid 92 through 106 removed outlier: 3.590A pdb=" N ILE F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 137 Processing helix chain 'F' and resid 161 through 172 removed outlier: 3.734A pdb=" N GLY F 165 " --> pdb=" O SER F 161 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 Processing helix chain 'H' and resid 22 through 27 Processing helix chain 'H' and resid 42 through 50 Processing sheet with id=AA1, first strand: chain 'V' and resid 38 through 43 removed outlier: 6.644A pdb=" N GLN V 87 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS V 88 " --> pdb=" O GLN V 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'V' and resid 61 through 65 Processing sheet with id=AA3, first strand: chain 'D' and resid 169 through 175 removed outlier: 3.595A pdb=" N SER D 174 " --> pdb=" O VAL D 107 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL D 107 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LYS D 8 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLU D 28 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL D 189 " --> pdb=" O THR D 25 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG D 179 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS D 190 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL D 177 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 79 through 83 removed outlier: 3.567A pdb=" N GLN D 36 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 117 through 119 Processing sheet with id=AA6, first strand: chain 'E' and resid 2 through 3 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.318A pdb=" N ILE E 119 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.860A pdb=" N TRP J 15 " --> pdb=" O GLN J 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 73 through 76 removed outlier: 3.677A pdb=" N HIS J 76 " --> pdb=" O LYS J 85 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS J 85 " --> pdb=" O HIS J 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 7 through 10 removed outlier: 6.233A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.868A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ILE P 63 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N GLY P 44 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE P 42 " --> pdb=" O VAL P 27 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL P 27 " --> pdb=" O PHE P 42 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY P 44 " --> pdb=" O VAL P 25 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N TRP P 30 " --> pdb=" O VAL P 80 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL P 80 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 89 through 90 removed outlier: 5.675A pdb=" N VAL L 122 " --> pdb=" O GLU L 143 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.529A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.512A pdb=" N TYR R 2 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 3.835A 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 23 removed outlier: 4.032A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS R 97 " --> pdb=" O VAL R 63 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N VAL R 63 " --> pdb=" O LYS R 97 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR R 99 " --> pdb=" O ALA R 61 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ALA R 61 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE R 101 " --> pdb=" O ILE R 59 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE R 59 " --> pdb=" O ILE R 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.359A 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: 3.841A pdb=" N HIS S 9 " --> pdb=" O SER S 101 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N SER S 101 " --> pdb=" O HIS S 9 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S' and resid 82 through 84 Processing sheet with id=AC1, first strand: chain 'T' and resid 11 through 14 removed outlier: 4.318A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'U' and resid 63 through 65 removed outlier: 6.761A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLU U 9 " --> pdb=" O PHE U 72 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'U' and resid 40 through 44 Processing sheet with id=AC4, first strand: chain 'U' and resid 82 through 85 removed outlier: 3.522A pdb=" N ARG U 85 " --> pdb=" O VAL U 92 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL U 92 " --> pdb=" O ARG U 85 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'X' and resid 12 through 15 removed outlier: 3.681A pdb=" N ARG X 26 " --> pdb=" O GLY X 14 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 32 through 39 Processing sheet with id=AC7, first strand: chain '0' and resid 28 through 29 Processing sheet with id=AC8, first strand: chain '0' and resid 47 through 48 Processing sheet with id=AC9, first strand: chain 'O' and resid 47 through 52 removed outlier: 4.230A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.952A pdb=" N GLY F 85 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N CYS F 86 " --> pdb=" O MET F 37 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR F 156 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE F 33 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR F 154 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU F 35 " --> pdb=" O ASP F 152 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ASP F 152 " --> pdb=" O LEU F 35 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR F 127 " --> pdb=" O ILE F 155 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Z' and resid 35 through 38 removed outlier: 4.157A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.881A pdb=" N ILE H 4 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL H 37 " --> pdb=" O ILE H 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'W' and resid 18 through 19 removed outlier: 3.860A pdb=" N GLY W 18 " --> pdb=" O ARG W 35 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG W 35 " --> pdb=" O GLY W 18 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU W 55 " --> pdb=" O ILE W 33 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'W' and resid 26 through 27 removed outlier: 6.335A pdb=" N HIS W 42 " --> pdb=" O ILE W 76 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N ILE W 78 " --> pdb=" O HIS W 42 " (cutoff:3.500A) 717 hydrogen bonds defined for protein. 2010 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1972 hydrogen bonds 3128 hydrogen bond angles 0 basepair planarities 777 basepair parallelities 1132 stacking parallelities Total time for adding SS restraints: 92.86 Time building geometry restraints manager: 34.00 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: 10780 1.33 - 1.45: 31329 1.45 - 1.57: 27356 1.57 - 1.69: 4639 1.69 - 1.81: 96 Bond restraints: 74200 Sorted by residual: bond pdb=" N LYS H 22 " pdb=" CA LYS H 22 " ideal model delta sigma weight residual 1.454 1.503 -0.049 1.29e-02 6.01e+03 1.43e+01 bond pdb=" N VAL H 19 " pdb=" CA VAL H 19 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.20e+01 bond pdb=" N ALA H 23 " pdb=" CA ALA H 23 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.20e-02 6.94e+03 8.90e+00 bond pdb=" N ILE T 2 " pdb=" CA ILE T 2 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.37e+00 bond pdb=" N ASN H 20 " pdb=" CA ASN H 20 " ideal model delta sigma weight residual 1.454 1.489 -0.036 1.34e-02 5.57e+03 7.05e+00 ... (remaining 74195 not shown) Histogram of bond angle deviations from ideal: 98.52 - 105.61: 11363 105.61 - 112.70: 43504 112.70 - 119.79: 25845 119.79 - 126.88: 24924 126.88 - 133.97: 6068 Bond angle restraints: 111704 Sorted by residual: angle pdb=" C3' G A2056 " pdb=" O3' G A2056 " pdb=" P G A2057 " ideal model delta sigma weight residual 120.20 105.06 15.14 1.50e+00 4.44e-01 1.02e+02 angle pdb=" C3' G A2057 " pdb=" O3' G A2057 " pdb=" P A A2058 " ideal model delta sigma weight residual 120.20 107.88 12.32 1.50e+00 4.44e-01 6.75e+01 angle pdb=" C3' A A2058 " pdb=" O3' A A2058 " pdb=" P A A2059 " ideal model delta sigma weight residual 120.20 109.16 11.04 1.50e+00 4.44e-01 5.41e+01 angle pdb=" C3' G A2061 " pdb=" O3' G A2061 " pdb=" P A A2062 " ideal model delta sigma weight residual 120.20 109.64 10.56 1.50e+00 4.44e-01 4.96e+01 angle pdb=" C3' A A2060 " pdb=" O3' A A2060 " pdb=" P G A2061 " ideal model delta sigma weight residual 120.20 109.82 10.38 1.50e+00 4.44e-01 4.79e+01 ... (remaining 111699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 41872 35.73 - 71.46: 5027 71.46 - 107.19: 626 107.19 - 142.93: 12 142.93 - 178.66: 4 Dihedral angle restraints: 47541 sinusoidal: 40969 harmonic: 6572 Sorted by residual: dihedral pdb=" O4' U A2884 " pdb=" C1' U A2884 " pdb=" N1 U A2884 " pdb=" C2 U A2884 " ideal model delta sinusoidal sigma weight residual -160.00 -35.17 -124.83 1 1.50e+01 4.44e-03 6.70e+01 dihedral pdb=" O4' U A1340 " pdb=" C1' U A1340 " pdb=" N1 U A1340 " pdb=" C2 U A1340 " ideal model delta sinusoidal sigma weight residual 232.00 54.78 177.22 1 1.70e+01 3.46e-03 6.64e+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 35.59 -163.59 1 1.70e+01 3.46e-03 6.51e+01 ... (remaining 47538 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 14068 0.084 - 0.168: 304 0.168 - 0.251: 8 0.251 - 0.335: 0 0.335 - 0.419: 13 Chirality restraints: 14393 Sorted by residual: chirality pdb=" P U A2244 " pdb=" OP1 U A2244 " pdb=" OP2 U A2244 " pdb=" O5' U A2244 " both_signs ideal model delta sigma weight residual True 2.41 -2.83 -0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" P A A2434 " pdb=" OP1 A A2434 " pdb=" OP2 A A2434 " pdb=" O5' A A2434 " both_signs ideal model delta sigma weight residual True 2.41 -2.82 -0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" P A A2058 " pdb=" OP1 A A2058 " pdb=" OP2 A A2058 " pdb=" O5' A A2058 " both_signs ideal model delta sigma weight residual True 2.41 -2.82 -0.41 2.00e-01 2.50e+01 4.21e+00 ... (remaining 14390 not shown) Planarity restraints: 5468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A2771 " 0.000 2.00e-02 2.50e+03 1.67e-02 6.29e+00 pdb=" N1 C A2771 " -0.002 2.00e-02 2.50e+03 pdb=" C2 C A2771 " -0.041 2.00e-02 2.50e+03 pdb=" O2 C A2771 " 0.027 2.00e-02 2.50e+03 pdb=" N3 C A2771 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C A2771 " -0.002 2.00e-02 2.50e+03 pdb=" N4 C A2771 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C A2771 " 0.006 2.00e-02 2.50e+03 pdb=" C6 C A2771 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1581 " 0.015 2.00e-02 2.50e+03 1.32e-02 5.25e+00 pdb=" N9 G A1581 " -0.016 2.00e-02 2.50e+03 pdb=" C8 G A1581 " -0.007 2.00e-02 2.50e+03 pdb=" N7 G A1581 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G A1581 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G A1581 " 0.015 2.00e-02 2.50e+03 pdb=" O6 G A1581 " -0.003 2.00e-02 2.50e+03 pdb=" N1 G A1581 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G A1581 " 0.028 2.00e-02 2.50e+03 pdb=" N2 G A1581 " -0.023 2.00e-02 2.50e+03 pdb=" N3 G A1581 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G A1581 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 51 " 0.009 2.00e-02 2.50e+03 1.16e-02 4.05e+00 pdb=" N9 G B 51 " -0.013 2.00e-02 2.50e+03 pdb=" C8 G B 51 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G B 51 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G B 51 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 51 " 0.007 2.00e-02 2.50e+03 pdb=" O6 G B 51 " -0.002 2.00e-02 2.50e+03 pdb=" N1 G B 51 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G B 51 " 0.029 2.00e-02 2.50e+03 pdb=" N2 G B 51 " -0.022 2.00e-02 2.50e+03 pdb=" N3 G B 51 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G B 51 " 0.000 2.00e-02 2.50e+03 ... (remaining 5465 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 484 2.49 - 3.09: 45433 3.09 - 3.69: 127519 3.69 - 4.30: 183284 4.30 - 4.90: 253128 Nonbonded interactions: 609848 Sorted by model distance: nonbonded pdb=" O2' G B 51 " pdb=" O4' A B 52 " model vdw 1.882 2.440 nonbonded pdb=" O GLY H 24 " pdb=" O ARG H 27 " model vdw 1.919 3.040 nonbonded pdb=" OP2 G A1125 " pdb=" O2' A A1126 " model vdw 1.923 2.440 nonbonded pdb=" OP2 U B 14 " pdb=" O2' C B 70 " model vdw 1.933 2.440 nonbonded pdb=" O2' G A 834 " pdb=" O2' A A2358 " model vdw 1.947 2.440 ... (remaining 609843 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 8.500 Check model and map are aligned: 0.800 Set scattering table: 0.490 Process input model: 237.810 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 253.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 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 0.049 74200 Z= 0.115 Angle : 0.424 15.142 111704 Z= 0.230 Chirality : 0.030 0.419 14393 Planarity : 0.003 0.059 5468 Dihedral : 22.598 178.656 43293 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.96 % Favored : 92.96 % Rotamer: Outliers : 0.05 % Allowed : 0.11 % Favored : 99.84 % 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: 0.01 (0.18), residues: 2257 helix: 1.43 (0.21), residues: 729 sheet: -0.18 (0.25), residues: 433 loop : -0.88 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP T 80 HIS 0.002 0.000 HIS Z 19 PHE 0.007 0.001 PHE U 95 TYR 0.009 0.001 TYR Q 31 ARG 0.008 0.000 ARG Q 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 300 time to evaluate : 2.848 Fit side-chains REVERT: V 50 MET cc_start: 0.4076 (mtt) cc_final: 0.3835 (mtt) REVERT: J 118 MET cc_start: 0.7541 (mtt) cc_final: 0.7326 (mtt) REVERT: K 20 MET cc_start: 0.6406 (tpp) cc_final: 0.6069 (tpp) REVERT: P 111 GLU cc_start: 0.6820 (mm-30) cc_final: 0.6596 (tp30) REVERT: R 70 GLU cc_start: 0.7933 (tt0) cc_final: 0.7677 (tt0) REVERT: X 10 ARG cc_start: 0.7129 (mtp85) cc_final: 0.6825 (mtt180) REVERT: X 38 TRP cc_start: 0.5749 (t60) cc_final: 0.5325 (t60) REVERT: O 3 LYS cc_start: 0.6926 (mmtt) cc_final: 0.6410 (mtmt) REVERT: O 8 ILE cc_start: 0.5903 (mm) cc_final: 0.5651 (mt) REVERT: W 76 ILE cc_start: 0.8762 (mm) cc_final: 0.8539 (mt) outliers start: 1 outliers final: 1 residues processed: 301 average time/residue: 0.7587 time to fit residues: 392.8169 Evaluate side-chains 207 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 206 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 382 optimal weight: 40.0000 chunk 343 optimal weight: 9.9990 chunk 190 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 231 optimal weight: 6.9990 chunk 183 optimal weight: 40.0000 chunk 355 optimal weight: 0.0040 chunk 137 optimal weight: 20.0000 chunk 215 optimal weight: 40.0000 chunk 264 optimal weight: 4.9990 chunk 411 optimal weight: 50.0000 overall best weight: 6.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 126 ASN J 77 HIS J 80 HIS K 82 ASN Q 43 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 74200 Z= 0.374 Angle : 0.657 11.199 111704 Z= 0.328 Chirality : 0.036 0.255 14393 Planarity : 0.005 0.050 5468 Dihedral : 23.196 178.503 38768 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.13 % Favored : 92.69 % Rotamer: Outliers : 1.86 % Allowed : 8.13 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.73 (0.17), residues: 2257 helix: 0.36 (0.19), residues: 724 sheet: -0.24 (0.24), residues: 439 loop : -1.13 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 78 HIS 0.012 0.002 HIS N 3 PHE 0.025 0.002 PHE Q 56 TYR 0.027 0.003 TYR Q 24 ARG 0.009 0.001 ARG Q 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 238 time to evaluate : 2.933 Fit side-chains revert: symmetry clash REVERT: K 1 MET cc_start: 0.7696 (pmm) cc_final: 0.7428 (pmm) REVERT: K 5 GLN cc_start: 0.6551 (tt0) cc_final: 0.6250 (tm-30) REVERT: Q 48 ASP cc_start: 0.8027 (m-30) cc_final: 0.7696 (m-30) REVERT: R 70 GLU cc_start: 0.8013 (tt0) cc_final: 0.7729 (tt0) REVERT: S 86 MET cc_start: 0.3979 (mtm) cc_final: 0.3620 (mtm) REVERT: S 109 ASP cc_start: 0.7400 (t0) cc_final: 0.7154 (t0) REVERT: X 10 ARG cc_start: 0.7441 (mtp85) cc_final: 0.7039 (mtt180) REVERT: X 29 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6662 (mt) REVERT: X 38 TRP cc_start: 0.6010 (t60) cc_final: 0.5543 (t60) REVERT: X 70 LEU cc_start: 0.6387 (mp) cc_final: 0.5951 (mp) REVERT: O 3 LYS cc_start: 0.6833 (mmtt) cc_final: 0.5963 (mtmt) outliers start: 35 outliers final: 26 residues processed: 258 average time/residue: 0.6667 time to fit residues: 295.4321 Evaluate side-chains 230 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 203 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain H residue 20 ASN Chi-restraints excluded: chain H residue 21 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 228 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 342 optimal weight: 5.9990 chunk 280 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 412 optimal weight: 30.0000 chunk 445 optimal weight: 0.0870 chunk 367 optimal weight: 5.9990 chunk 408 optimal weight: 20.0000 chunk 140 optimal weight: 40.0000 chunk 330 optimal weight: 0.8980 overall best weight: 4.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 51 GLN K 82 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 GLN ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN 0 5 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 74200 Z= 0.243 Angle : 0.530 10.348 111704 Z= 0.269 Chirality : 0.031 0.233 14393 Planarity : 0.004 0.055 5468 Dihedral : 23.169 176.473 38768 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.09 % Favored : 92.78 % Rotamer: Outliers : 2.34 % Allowed : 11.69 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.74 (0.17), residues: 2257 helix: 0.43 (0.20), residues: 728 sheet: -0.40 (0.24), residues: 443 loop : -1.13 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP T 80 HIS 0.008 0.001 HIS N 3 PHE 0.018 0.002 PHE V 91 TYR 0.020 0.002 TYR S 38 ARG 0.008 0.001 ARG O 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 230 time to evaluate : 2.938 Fit side-chains REVERT: V 75 GLN cc_start: 0.6551 (pm20) cc_final: 0.6290 (pm20) REVERT: K 5 GLN cc_start: 0.6506 (tt0) cc_final: 0.6246 (tm-30) REVERT: N 70 THR cc_start: 0.8721 (p) cc_final: 0.8392 (p) REVERT: R 70 GLU cc_start: 0.8011 (tt0) cc_final: 0.7738 (tt0) REVERT: S 86 MET cc_start: 0.3976 (mtm) cc_final: 0.3601 (mtm) REVERT: U 53 GLN cc_start: 0.5655 (mp10) cc_final: 0.5420 (pm20) REVERT: X 29 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6601 (mt) REVERT: X 38 TRP cc_start: 0.5970 (t60) cc_final: 0.5290 (t60) REVERT: O 3 LYS cc_start: 0.6758 (mmtt) cc_final: 0.5848 (mtmt) REVERT: Z 46 MET cc_start: 0.8073 (mtt) cc_final: 0.7681 (mtm) outliers start: 44 outliers final: 32 residues processed: 255 average time/residue: 0.6657 time to fit residues: 291.5951 Evaluate side-chains 239 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 206 time to evaluate : 2.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 11 GLN Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain H residue 20 ASN Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 40 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 407 optimal weight: 20.0000 chunk 309 optimal weight: 8.9990 chunk 213 optimal weight: 40.0000 chunk 45 optimal weight: 30.0000 chunk 196 optimal weight: 30.0000 chunk 276 optimal weight: 3.9990 chunk 413 optimal weight: 20.0000 chunk 437 optimal weight: 0.9980 chunk 216 optimal weight: 10.0000 chunk 391 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 82 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.145 74200 Z= 0.345 Angle : 0.625 9.792 111704 Z= 0.315 Chirality : 0.035 0.259 14393 Planarity : 0.005 0.056 5468 Dihedral : 23.253 179.606 38768 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.98 % Favored : 91.89 % Rotamer: Outliers : 3.88 % Allowed : 12.17 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.17), residues: 2257 helix: 0.09 (0.19), residues: 720 sheet: -0.77 (0.23), residues: 470 loop : -1.19 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 78 HIS 0.006 0.001 HIS R 12 PHE 0.018 0.002 PHE Q 56 TYR 0.025 0.002 TYR S 38 ARG 0.007 0.001 ARG S 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 224 time to evaluate : 3.317 Fit side-chains revert: symmetry clash REVERT: V 75 GLN cc_start: 0.6582 (pm20) cc_final: 0.6081 (pm20) REVERT: K 5 GLN cc_start: 0.6497 (tt0) cc_final: 0.6159 (tm-30) REVERT: K 20 MET cc_start: 0.6610 (tpp) cc_final: 0.6398 (tpp) REVERT: R 25 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7461 (pp) REVERT: R 70 GLU cc_start: 0.7981 (tt0) cc_final: 0.7682 (tt0) REVERT: S 109 ASP cc_start: 0.7287 (t0) cc_final: 0.7048 (t0) REVERT: X 27 ARG cc_start: 0.6932 (ttp-170) cc_final: 0.6665 (mtp180) REVERT: X 38 TRP cc_start: 0.6021 (t60) cc_final: 0.5077 (t60) REVERT: Y 12 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7436 (pt0) REVERT: O 3 LYS cc_start: 0.6654 (mmtt) cc_final: 0.5636 (mtmt) outliers start: 73 outliers final: 56 residues processed: 276 average time/residue: 0.7524 time to fit residues: 363.0161 Evaluate side-chains 263 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 205 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain U residue 102 ILE Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 12 GLU Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain H residue 20 ASN Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain W residue 17 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 364 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 326 optimal weight: 5.9990 chunk 180 optimal weight: 40.0000 chunk 373 optimal weight: 1.9990 chunk 302 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 223 optimal weight: 10.0000 chunk 393 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 82 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 74200 Z= 0.215 Angle : 0.530 10.259 111704 Z= 0.270 Chirality : 0.031 0.253 14393 Planarity : 0.004 0.058 5468 Dihedral : 23.221 177.969 38768 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.18 % Favored : 92.69 % Rotamer: Outliers : 3.77 % Allowed : 12.75 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.17), residues: 2257 helix: 0.27 (0.20), residues: 726 sheet: -0.66 (0.24), residues: 455 loop : -1.20 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP T 80 HIS 0.004 0.001 HIS N 3 PHE 0.012 0.001 PHE V 91 TYR 0.019 0.002 TYR S 38 ARG 0.005 0.000 ARG V 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 224 time to evaluate : 2.910 Fit side-chains revert: symmetry clash REVERT: V 75 GLN cc_start: 0.6120 (pm20) cc_final: 0.5730 (pm20) REVERT: E 1 MET cc_start: 0.6838 (pmm) cc_final: 0.6633 (pmm) REVERT: J 1 MET cc_start: 0.6934 (OUTLIER) cc_final: 0.6562 (ptm) REVERT: K 5 GLN cc_start: 0.6793 (tt0) cc_final: 0.6475 (tt0) REVERT: R 70 GLU cc_start: 0.7991 (tt0) cc_final: 0.7705 (tt0) REVERT: S 109 ASP cc_start: 0.7344 (t0) cc_final: 0.7083 (t0) REVERT: X 38 TRP cc_start: 0.5959 (t60) cc_final: 0.5065 (t60) REVERT: O 3 LYS cc_start: 0.6725 (mmtt) cc_final: 0.5779 (mtmt) outliers start: 71 outliers final: 53 residues processed: 278 average time/residue: 0.6588 time to fit residues: 315.6739 Evaluate side-chains 263 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 209 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 20 ASN Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 40 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 147 optimal weight: 20.0000 chunk 394 optimal weight: 3.9990 chunk 86 optimal weight: 40.0000 chunk 257 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 438 optimal weight: 3.9990 chunk 363 optimal weight: 4.9990 chunk 202 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 144 optimal weight: 20.0000 chunk 230 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 90 GLN K 82 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 74200 Z= 0.290 Angle : 0.579 10.311 111704 Z= 0.294 Chirality : 0.033 0.257 14393 Planarity : 0.004 0.057 5468 Dihedral : 23.234 178.740 38768 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.24 % Favored : 91.63 % Rotamer: Outliers : 4.25 % Allowed : 13.18 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.05 (0.17), residues: 2257 helix: 0.09 (0.19), residues: 726 sheet: -0.69 (0.24), residues: 459 loop : -1.19 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 78 HIS 0.005 0.001 HIS N 3 PHE 0.014 0.002 PHE Q 56 TYR 0.023 0.002 TYR S 38 ARG 0.007 0.001 ARG 2 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 223 time to evaluate : 2.916 Fit side-chains REVERT: V 50 MET cc_start: 0.5864 (mtt) cc_final: 0.5405 (mtt) REVERT: V 75 GLN cc_start: 0.6142 (pm20) cc_final: 0.5780 (pm20) REVERT: J 1 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6602 (ptm) REVERT: K 106 GLU cc_start: 0.6006 (mp0) cc_final: 0.5492 (tm-30) REVERT: R 70 GLU cc_start: 0.7947 (tt0) cc_final: 0.7666 (tt0) REVERT: X 38 TRP cc_start: 0.6025 (t60) cc_final: 0.5107 (t60) REVERT: Y 12 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7481 (pt0) REVERT: O 3 LYS cc_start: 0.6585 (mmtt) cc_final: 0.5593 (mtmt) REVERT: H 33 GLN cc_start: 0.0382 (OUTLIER) cc_final: -0.2223 (tp40) outliers start: 80 outliers final: 68 residues processed: 281 average time/residue: 0.6508 time to fit residues: 317.2800 Evaluate side-chains 280 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 209 time to evaluate : 2.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 12 GLU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 20 ASN Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain W residue 17 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 422 optimal weight: 50.0000 chunk 49 optimal weight: 20.0000 chunk 249 optimal weight: 4.9990 chunk 320 optimal weight: 10.0000 chunk 247 optimal weight: 0.9990 chunk 368 optimal weight: 3.9990 chunk 244 optimal weight: 0.0030 chunk 436 optimal weight: 40.0000 chunk 273 optimal weight: 4.9990 chunk 266 optimal weight: 0.0370 chunk 201 optimal weight: 10.0000 overall best weight: 2.0074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 90 GLN K 82 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 74200 Z= 0.143 Angle : 0.493 10.932 111704 Z= 0.253 Chirality : 0.029 0.247 14393 Planarity : 0.004 0.058 5468 Dihedral : 23.206 179.801 38768 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.78 % Favored : 93.09 % Rotamer: Outliers : 3.03 % Allowed : 14.93 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.17), residues: 2257 helix: 0.39 (0.20), residues: 718 sheet: -0.54 (0.24), residues: 447 loop : -1.13 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP T 80 HIS 0.007 0.001 HIS 2 16 PHE 0.010 0.001 PHE E 183 TYR 0.018 0.001 TYR S 38 ARG 0.006 0.000 ARG 2 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 226 time to evaluate : 2.918 Fit side-chains REVERT: V 50 MET cc_start: 0.5585 (mtt) cc_final: 0.5159 (mtt) REVERT: V 75 GLN cc_start: 0.5948 (pm20) cc_final: 0.5549 (pm20) REVERT: K 106 GLU cc_start: 0.5916 (mp0) cc_final: 0.5626 (tm-30) REVERT: K 108 ARG cc_start: 0.5995 (mtm180) cc_final: 0.5760 (tmm160) REVERT: N 70 THR cc_start: 0.8624 (p) cc_final: 0.8209 (p) REVERT: X 27 ARG cc_start: 0.7492 (mtp180) cc_final: 0.6908 (ttp-170) REVERT: X 38 TRP cc_start: 0.5807 (t60) cc_final: 0.4892 (t60) REVERT: O 3 LYS cc_start: 0.6570 (mmtt) cc_final: 0.5737 (mtmt) REVERT: F 141 ASP cc_start: 0.5133 (t70) cc_final: 0.4791 (t70) REVERT: H 33 GLN cc_start: 0.0247 (OUTLIER) cc_final: -0.2265 (tp40) outliers start: 57 outliers final: 50 residues processed: 272 average time/residue: 0.6465 time to fit residues: 306.0142 Evaluate side-chains 262 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 211 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 20 ASN Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 40 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 270 optimal weight: 0.6980 chunk 174 optimal weight: 40.0000 chunk 260 optimal weight: 5.9990 chunk 131 optimal weight: 40.0000 chunk 85 optimal weight: 40.0000 chunk 84 optimal weight: 20.0000 chunk 277 optimal weight: 4.9990 chunk 297 optimal weight: 20.0000 chunk 215 optimal weight: 40.0000 chunk 40 optimal weight: 10.0000 chunk 343 optimal weight: 7.9990 overall best weight: 5.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN K 82 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN T 48 GLN ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 74200 Z= 0.319 Angle : 0.593 11.206 111704 Z= 0.299 Chirality : 0.034 0.262 14393 Planarity : 0.004 0.056 5468 Dihedral : 23.228 178.892 38768 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.29 % Favored : 91.58 % Rotamer: Outliers : 3.45 % Allowed : 14.93 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.05 (0.17), residues: 2257 helix: 0.18 (0.20), residues: 714 sheet: -0.69 (0.24), residues: 459 loop : -1.25 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP T 80 HIS 0.005 0.001 HIS 2 16 PHE 0.013 0.002 PHE Q 56 TYR 0.024 0.002 TYR S 38 ARG 0.006 0.001 ARG V 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 216 time to evaluate : 2.914 Fit side-chains REVERT: V 50 MET cc_start: 0.5667 (mtt) cc_final: 0.5260 (mtt) REVERT: K 5 GLN cc_start: 0.6229 (tt0) cc_final: 0.6007 (tm-30) REVERT: K 106 GLU cc_start: 0.6149 (mp0) cc_final: 0.5931 (tm-30) REVERT: Q 48 ASP cc_start: 0.7840 (m-30) cc_final: 0.7559 (m-30) REVERT: R 70 GLU cc_start: 0.7945 (tt0) cc_final: 0.7661 (tt0) REVERT: X 38 TRP cc_start: 0.5796 (t60) cc_final: 0.4953 (t60) REVERT: O 3 LYS cc_start: 0.6468 (mmtt) cc_final: 0.5570 (mtmt) REVERT: F 141 ASP cc_start: 0.5098 (t70) cc_final: 0.4793 (t70) REVERT: H 33 GLN cc_start: 0.0056 (OUTLIER) cc_final: -0.2446 (mm-40) outliers start: 65 outliers final: 57 residues processed: 267 average time/residue: 0.6500 time to fit residues: 301.7003 Evaluate side-chains 267 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 209 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 20 ASN Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 40 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 397 optimal weight: 3.9990 chunk 418 optimal weight: 7.9990 chunk 381 optimal weight: 5.9990 chunk 406 optimal weight: 30.0000 chunk 244 optimal weight: 6.9990 chunk 177 optimal weight: 40.0000 chunk 319 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 367 optimal weight: 0.7980 chunk 384 optimal weight: 2.9990 chunk 405 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 82 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN T 91 GLN ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 74200 Z= 0.224 Angle : 0.539 12.278 111704 Z= 0.274 Chirality : 0.032 0.253 14393 Planarity : 0.004 0.057 5468 Dihedral : 23.229 178.688 38767 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.49 % Favored : 92.38 % Rotamer: Outliers : 3.08 % Allowed : 15.99 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.17), residues: 2257 helix: 0.26 (0.20), residues: 715 sheet: -0.68 (0.24), residues: 457 loop : -1.21 (0.18), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP T 80 HIS 0.006 0.001 HIS 2 16 PHE 0.011 0.001 PHE E 183 TYR 0.022 0.002 TYR S 38 ARG 0.006 0.001 ARG 2 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 215 time to evaluate : 2.945 Fit side-chains REVERT: V 50 MET cc_start: 0.5644 (mtt) cc_final: 0.5244 (mtt) REVERT: Q 48 ASP cc_start: 0.7809 (m-30) cc_final: 0.7570 (m-30) REVERT: T 91 GLN cc_start: 0.7460 (mm110) cc_final: 0.7036 (mm-40) REVERT: X 38 TRP cc_start: 0.5705 (t60) cc_final: 0.4808 (t60) REVERT: O 3 LYS cc_start: 0.6588 (mmtt) cc_final: 0.5718 (mtmt) REVERT: F 95 MET cc_start: 0.4991 (ptt) cc_final: 0.4731 (ptm) REVERT: F 141 ASP cc_start: 0.5039 (t70) cc_final: 0.4752 (t70) REVERT: H 33 GLN cc_start: 0.0205 (OUTLIER) cc_final: -0.2361 (mm-40) outliers start: 58 outliers final: 54 residues processed: 263 average time/residue: 0.6767 time to fit residues: 310.0796 Evaluate side-chains 263 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 208 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 20 ASN Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 40 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 267 optimal weight: 1.9990 chunk 430 optimal weight: 40.0000 chunk 262 optimal weight: 5.9990 chunk 204 optimal weight: 30.0000 chunk 299 optimal weight: 9.9990 chunk 451 optimal weight: 5.9990 chunk 415 optimal weight: 30.0000 chunk 359 optimal weight: 9.9990 chunk 37 optimal weight: 30.0000 chunk 277 optimal weight: 2.9990 chunk 220 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 82 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 74200 Z= 0.298 Angle : 0.586 15.821 111704 Z= 0.296 Chirality : 0.034 0.261 14393 Planarity : 0.004 0.057 5468 Dihedral : 23.260 178.858 38767 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.68 % Favored : 91.18 % Rotamer: Outliers : 3.29 % Allowed : 15.78 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.13 (0.17), residues: 2257 helix: 0.11 (0.20), residues: 721 sheet: -0.76 (0.24), residues: 450 loop : -1.29 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 78 HIS 0.005 0.001 HIS 2 16 PHE 0.012 0.002 PHE E 183 TYR 0.022 0.002 TYR S 38 ARG 0.007 0.001 ARG V 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4514 Ramachandran restraints generated. 2257 Oldfield, 0 Emsley, 2257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 211 time to evaluate : 3.008 Fit side-chains REVERT: V 50 MET cc_start: 0.5803 (mtt) cc_final: 0.5376 (mtt) REVERT: K 108 ARG cc_start: 0.6029 (mtm180) cc_final: 0.5772 (tmm160) REVERT: Q 48 ASP cc_start: 0.7866 (m-30) cc_final: 0.7628 (m-30) REVERT: T 91 GLN cc_start: 0.7611 (mm110) cc_final: 0.7159 (mm-40) REVERT: X 38 TRP cc_start: 0.5725 (t60) cc_final: 0.4832 (t60) REVERT: O 3 LYS cc_start: 0.6430 (mmtt) cc_final: 0.5524 (mtmt) REVERT: F 86 CYS cc_start: 0.4760 (p) cc_final: 0.3787 (m) REVERT: F 95 MET cc_start: 0.5000 (ptt) cc_final: 0.4739 (ptm) REVERT: F 141 ASP cc_start: 0.5108 (t70) cc_final: 0.4793 (t70) REVERT: H 33 GLN cc_start: 0.0271 (OUTLIER) cc_final: -0.2344 (mm-40) outliers start: 62 outliers final: 60 residues processed: 260 average time/residue: 0.6642 time to fit residues: 300.0305 Evaluate side-chains 267 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 206 time to evaluate : 2.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 20 ASN Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 40 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 285 optimal weight: 0.6980 chunk 382 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 331 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 99 optimal weight: 20.0000 chunk 359 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 369 optimal weight: 0.8980 chunk 45 optimal weight: 30.0000 chunk 66 optimal weight: 10.0000 overall best weight: 4.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 82 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.098720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.069984 restraints weight = 244415.642| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.58 r_work: 0.3133 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 74200 Z= 0.252 Angle : 0.557 14.010 111704 Z= 0.282 Chirality : 0.033 0.255 14393 Planarity : 0.004 0.057 5468 Dihedral : 23.265 178.509 38767 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.93 % Favored : 91.94 % Rotamer: Outliers : 3.19 % Allowed : 16.42 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.17), residues: 2257 helix: 0.11 (0.20), residues: 727 sheet: -0.75 (0.24), residues: 450 loop : -1.27 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP T 80 HIS 0.006 0.001 HIS 2 16 PHE 0.012 0.001 PHE E 183 TYR 0.022 0.002 TYR S 38 ARG 0.007 0.001 ARG Y 7 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9172.03 seconds wall clock time: 166 minutes 33.53 seconds (9993.53 seconds total)