Starting phenix.real_space_refine on Fri Mar 22 18:53:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o5h_12736/03_2024/7o5h_12736.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o5h_12736/03_2024/7o5h_12736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o5h_12736/03_2024/7o5h_12736.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o5h_12736/03_2024/7o5h_12736.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o5h_12736/03_2024/7o5h_12736.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o5h_12736/03_2024/7o5h_12736.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 964 5.49 5 Mg 167 5.21 5 S 59 5.16 5 C 17729 2.51 5 N 6377 2.21 5 O 9140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "V PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 169": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34436 Number of models: 1 Model: "" Number of chains: 22 Chain: "V" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1955 Classifications: {'peptide': 251} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 231} Chain: "A" Number of atoms: 20726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 20726 Classifications: {'RNA': 964} Modifications used: {'rna2p_pur': 78, 'rna2p_pyr': 44, 'rna3p_pur': 485, 'rna3p_pyr': 357} Link IDs: {'rna2p': 121, 'rna3p': 842} Chain breaks: 7 Chain: "B" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1165 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "F" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 839 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "O" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 702 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 641 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 456 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 252 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "A" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Unusual residues: {' MG': 161} Classifications: {'undetermined': 161} Link IDs: {None: 160} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 29871 SG CYS K 121 97.455 45.225 110.621 1.00 55.55 S Time building chain proxies: 17.90, per 1000 atoms: 0.52 Number of scatterers: 34436 At special positions: 0 Unit cell: (168.19, 191.82, 159.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 59 16.00 P 964 15.00 Mg 167 11.99 O 9140 8.00 N 6377 7.00 C 17729 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: 18.56 Conformation dependent library (CDL) restraints added in 2.9 seconds 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3214 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 15 sheets defined 46.6% alpha, 18.9% beta 317 base pairs and 590 stacking pairs defined. Time for finding SS restraints: 15.55 Creating SS restraints... Processing helix chain 'V' and resid 22 through 34 Processing helix chain 'V' and resid 51 through 56 removed outlier: 3.846A pdb=" N VAL V 55 " --> pdb=" O LEU V 51 " (cutoff:3.500A) Processing helix chain 'V' and resid 68 through 77 Processing helix chain 'V' and resid 96 through 105 removed outlier: 4.495A pdb=" N LEU V 100 " --> pdb=" O ASN V 96 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA V 101 " --> pdb=" O PHE V 97 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU V 102 " --> pdb=" O GLY V 98 " (cutoff:3.500A) Processing helix chain 'V' and resid 115 through 128 removed outlier: 4.439A pdb=" N THR V 120 " --> pdb=" O TYR V 116 " (cutoff:3.500A) Proline residue: V 121 - end of helix Processing helix chain 'V' and resid 141 through 150 Processing helix chain 'V' and resid 158 through 167 removed outlier: 4.308A pdb=" N TYR V 167 " --> pdb=" O MET V 163 " (cutoff:3.500A) Processing helix chain 'V' and resid 177 through 179 No H-bonds generated for 'chain 'V' and resid 177 through 179' Processing helix chain 'V' and resid 206 through 218 Processing helix chain 'V' and resid 219 through 221 No H-bonds generated for 'chain 'V' and resid 219 through 221' Processing helix chain 'V' and resid 224 through 229 Processing helix chain 'V' and resid 234 through 241 Processing helix chain 'V' and resid 248 through 252 Processing helix chain 'V' and resid 253 through 268 Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 24 through 29 Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 42 through 63 removed outlier: 3.587A pdb=" N THR B 46 " --> pdb=" O ASN B 42 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 73 through 87 removed outlier: 4.359A pdb=" N GLU B 78 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 85 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 123 removed outlier: 3.621A pdb=" N SER B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 149 Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 169 through 180 Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.626A pdb=" N GLY B 195 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 227 removed outlier: 3.762A pdb=" N THR B 220 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 16 removed outlier: 4.207A pdb=" N LEU D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.778A pdb=" N LYS D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 43 removed outlier: 4.456A pdb=" N ALA D 43 " --> pdb=" O GLN D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 68 through 82 Processing helix chain 'D' and resid 85 through 96 Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 147 through 150 Processing helix chain 'D' and resid 152 through 165 removed outlier: 3.752A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 206 Processing helix chain 'E' and resid 55 through 69 removed outlier: 3.597A pdb=" N ARG E 69 " --> pdb=" O GLU E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 119 removed outlier: 3.676A pdb=" N ALA E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 146 removed outlier: 3.712A pdb=" N ASN E 146 " --> pdb=" O ASP E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 157 Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'F' and resid 12 through 16 removed outlier: 4.934A pdb=" N GLU F 16 " --> pdb=" O ASP F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 32 removed outlier: 3.518A pdb=" N ARG F 24 " --> pdb=" O GLY F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 80 removed outlier: 3.551A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 20 removed outlier: 3.524A pdb=" N ASP H 9 " --> pdb=" O ASP H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 44 Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'H' and resid 94 through 99 removed outlier: 3.679A pdb=" N ALA H 97 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 120 Processing helix chain 'K' and resid 48 through 51 removed outlier: 3.879A pdb=" N GLY K 51 " --> pdb=" O GLY K 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 48 through 51' Processing helix chain 'K' and resid 59 through 75 removed outlier: 3.615A pdb=" N ALA K 63 " --> pdb=" O THR K 59 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU K 68 " --> pdb=" O GLN K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 78 No H-bonds generated for 'chain 'K' and resid 76 through 78' Processing helix chain 'K' and resid 92 through 103 removed outlier: 3.574A pdb=" N THR K 96 " --> pdb=" O GLY K 92 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 113 through 117 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 46 removed outlier: 4.263A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.750A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'P' and resid 53 through 63 Processing helix chain 'P' and resid 68 through 82 Processing helix chain 'Q' and resid 49 through 52 removed outlier: 3.929A pdb=" N GLU Q 52 " --> pdb=" O GLU Q 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 49 through 52' Processing helix chain 'R' and resid 25 through 31 removed outlier: 3.805A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 removed outlier: 3.587A pdb=" N THR R 45 " --> pdb=" O PRO R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 65 Processing helix chain 'T' and resid 4 through 42 removed outlier: 3.506A pdb=" N ARG T 24 " --> pdb=" O HIS T 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 64 removed outlier: 3.622A pdb=" N ALA T 47 " --> pdb=" O ASP T 43 " (cutoff:3.500A) Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 87 Processing helix chain 'U' and resid 29 through 36 removed outlier: 3.578A pdb=" N ARG U 33 " --> pdb=" O LEU U 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG U 34 " --> pdb=" O ALA U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 55 Processing sheet with id=AA1, first strand: chain 'V' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'V' and resid 85 through 89 removed outlier: 3.546A pdb=" N PHE V 111 " --> pdb=" O VAL V 42 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE V 44 " --> pdb=" O PHE V 111 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU V 108 " --> pdb=" O ASP V 135 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N HIS V 137 " --> pdb=" O LEU V 108 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL V 110 " --> pdb=" O HIS V 137 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N MET V 139 " --> pdb=" O VAL V 110 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ALA V 134 " --> pdb=" O PRO V 196 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG V 193 " --> pdb=" O PRO V 172 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL V 195 " --> pdb=" O VAL V 170 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N VAL V 170 " --> pdb=" O VAL V 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 16 through 19 removed outlier: 5.552A pdb=" N PHE B 16 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ILE B 41 " --> pdb=" O PHE B 16 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N HIS B 18 " --> pdb=" O HIS B 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.268A pdb=" N LEU B 68 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE B 164 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL B 70 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL B 183 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE B 200 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA B 185 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 128 through 129 removed outlier: 3.849A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 12 through 24 removed outlier: 5.001A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 85 through 88 removed outlier: 6.465A pdb=" N ILE E 106 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ALA E 127 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 35 through 51 removed outlier: 5.000A pdb=" N ILE F 36 " --> pdb=" O GLU F 65 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU F 65 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG F 38 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG F 44 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA F 57 " --> pdb=" O ARG F 44 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLN F 46 " --> pdb=" O HIS F 55 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N HIS F 55 " --> pdb=" O GLN F 46 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 24 through 28 Processing sheet with id=AB1, first strand: chain 'H' and resid 74 through 77 Processing sheet with id=AB2, first strand: chain 'H' and resid 74 through 77 removed outlier: 6.845A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 41 through 46 removed outlier: 6.681A pdb=" N ILE K 34 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TRP K 44 " --> pdb=" O VAL K 32 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL K 32 " --> pdb=" O TRP K 44 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR K 46 " --> pdb=" O THR K 30 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR K 30 " --> pdb=" O THR K 46 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU K 82 " --> pdb=" O ILE K 107 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASN K 109 " --> pdb=" O LEU K 82 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 62 through 66 removed outlier: 3.545A pdb=" N ARG L 36 " --> pdb=" O ARG L 54 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG L 56 " --> pdb=" O CYS L 34 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N CYS L 34 " --> pdb=" O ARG L 56 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS L 30 " --> pdb=" O ILE L 82 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER L 78 " --> pdb=" O CYS L 34 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'P' and resid 50 through 52 removed outlier: 6.638A pdb=" N VAL P 19 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE P 38 " --> pdb=" O TYR P 17 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR P 17 " --> pdb=" O PHE P 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Q' and resid 8 through 14 removed outlier: 7.521A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N LYS Q 71 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N HIS Q 45 " --> pdb=" O LYS Q 71 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TRP Q 73 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU Q 75 " --> pdb=" O HIS Q 47 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N LEU Q 75 " --> pdb=" O ARG Q 62 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ARG Q 62 " --> pdb=" O LEU Q 75 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG Q 77 " --> pdb=" O GLU Q 60 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1899 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 778 hydrogen bonds 1242 hydrogen bond angles 0 basepair planarities 317 basepair parallelities 590 stacking parallelities Total time for adding SS restraints: 27.04 Time building geometry restraints manager: 19.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6692 1.33 - 1.45: 13488 1.45 - 1.57: 14758 1.57 - 1.69: 1920 1.69 - 1.81: 105 Bond restraints: 36963 Sorted by residual: bond pdb=" C3' A A 411 " pdb=" O3' A A 411 " ideal model delta sigma weight residual 1.427 1.445 -0.018 1.50e-02 4.44e+03 1.37e+00 bond pdb=" CA VAL F 18 " pdb=" CB VAL F 18 " ideal model delta sigma weight residual 1.539 1.545 -0.006 5.40e-03 3.43e+04 1.21e+00 bond pdb=" CA VAL B 47 " pdb=" CB VAL B 47 " ideal model delta sigma weight residual 1.539 1.544 -0.005 5.40e-03 3.43e+04 1.03e+00 bond pdb=" C VAL V 110 " pdb=" N PHE V 111 " ideal model delta sigma weight residual 1.333 1.345 -0.012 1.30e-02 5.92e+03 8.83e-01 bond pdb=" CA VAL H 72 " pdb=" CB VAL H 72 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.05e-02 9.07e+03 6.75e-01 ... (remaining 36958 not shown) Histogram of bond angle deviations from ideal: 100.20 - 106.95: 6048 106.95 - 113.70: 22319 113.70 - 120.45: 13449 120.45 - 127.20: 10709 127.20 - 133.95: 2182 Bond angle restraints: 54707 Sorted by residual: angle pdb=" C3' A A 411 " pdb=" O3' A A 411 " pdb=" P A A 412 " ideal model delta sigma weight residual 120.20 125.15 -4.95 1.50e+00 4.44e-01 1.09e+01 angle pdb=" C4' A A 411 " pdb=" C3' A A 411 " pdb=" O3' A A 411 " ideal model delta sigma weight residual 109.40 113.03 -3.63 1.50e+00 4.44e-01 5.84e+00 angle pdb=" O3' A A 411 " pdb=" C3' A A 411 " pdb=" C2' A A 411 " ideal model delta sigma weight residual 109.50 113.02 -3.52 1.50e+00 4.44e-01 5.50e+00 angle pdb=" C3' C A1107 " pdb=" O3' C A1107 " pdb=" P G A1108 " ideal model delta sigma weight residual 120.20 123.42 -3.22 1.50e+00 4.44e-01 4.60e+00 angle pdb=" O3' C A1107 " pdb=" C3' C A1107 " pdb=" C2' C A1107 " ideal model delta sigma weight residual 113.70 116.70 -3.00 1.50e+00 4.44e-01 4.01e+00 ... (remaining 54702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 21079 35.58 - 71.16: 2239 71.16 - 106.74: 250 106.74 - 142.32: 0 142.32 - 177.89: 7 Dihedral angle restraints: 23575 sinusoidal: 18602 harmonic: 4973 Sorted by residual: dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 53.36 146.64 1 1.50e+01 4.44e-03 7.83e+01 dihedral pdb=" O4' C A 754 " pdb=" C1' C A 754 " pdb=" N1 C A 754 " pdb=" C2 C A 754 " ideal model delta sinusoidal sigma weight residual 200.00 57.36 142.64 1 1.50e+01 4.44e-03 7.66e+01 dihedral pdb=" O4' C A 183 " pdb=" C1' C A 183 " pdb=" N1 C A 183 " pdb=" C2 C A 183 " ideal model delta sinusoidal sigma weight residual 232.00 54.11 177.89 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 23572 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 6324 0.041 - 0.081: 399 0.081 - 0.122: 163 0.122 - 0.163: 12 0.163 - 0.204: 1 Chirality restraints: 6899 Sorted by residual: chirality pdb=" C3' A A 411 " pdb=" C4' A A 411 " pdb=" O3' A A 411 " pdb=" C2' A A 411 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C3' C A1107 " pdb=" C4' C A1107 " pdb=" O3' C A1107 " pdb=" C2' C A1107 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.16 2.00e-01 2.50e+01 6.61e-01 chirality pdb=" C1' U A 365 " pdb=" O4' U A 365 " pdb=" C2' U A 365 " pdb=" N1 U A 365 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.15 2.00e-01 2.50e+01 5.92e-01 ... (remaining 6896 not shown) Planarity restraints: 3369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS L 44 " -0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO L 45 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO L 45 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO L 45 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 138 " -0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO D 139 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO D 139 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 139 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 80 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO H 81 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO H 81 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 81 " 0.016 5.00e-02 4.00e+02 ... (remaining 3366 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 4 1.99 - 2.72: 2835 2.72 - 3.44: 46149 3.44 - 4.17: 112281 4.17 - 4.90: 155292 Nonbonded interactions: 316561 Sorted by model distance: nonbonded pdb="MG MG A1632 " pdb="MG MG A1696 " model vdw 1.262 1.300 nonbonded pdb=" OP1 C A 504 " pdb="MG MG A1725 " model vdw 1.933 2.170 nonbonded pdb=" OP2 A A 195 " pdb="MG MG A1642 " model vdw 1.976 2.170 nonbonded pdb=" OP1 A A 59 " pdb="MG MG A1621 " model vdw 1.983 2.170 nonbonded pdb=" O4' G A 713 " pdb="MG MG A1708 " model vdw 2.009 2.170 ... (remaining 316556 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: 0.000 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: 0.030 Extract box with map and model: 8.560 Check model and map are aligned: 0.560 Set scattering table: 0.350 Process input model: 115.560 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 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 0.035 36963 Z= 0.108 Angle : 0.328 5.327 54707 Z= 0.176 Chirality : 0.025 0.204 6899 Planarity : 0.003 0.030 3369 Dihedral : 21.625 177.894 20361 Min Nonbonded Distance : 1.262 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.98 % Allowed : 3.07 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.21), residues: 1702 helix: 1.77 (0.20), residues: 682 sheet: 0.14 (0.31), residues: 301 loop : 0.07 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 23 HIS 0.003 0.001 HIS E 89 PHE 0.008 0.001 PHE V 111 TYR 0.007 0.001 TYR L 95 ARG 0.003 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 413 time to evaluate : 2.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 23 GLN cc_start: 0.6955 (tp40) cc_final: 0.6617 (tp-100) REVERT: V 44 ILE cc_start: 0.6889 (mm) cc_final: 0.6495 (mt) REVERT: V 48 LEU cc_start: 0.8249 (tp) cc_final: 0.7819 (tt) REVERT: V 170 VAL cc_start: 0.8201 (t) cc_final: 0.7934 (p) REVERT: V 257 TYR cc_start: 0.8370 (m-80) cc_final: 0.8024 (m-80) REVERT: B 147 SER cc_start: 0.8068 (m) cc_final: 0.7784 (p) REVERT: B 168 HIS cc_start: 0.7716 (t-90) cc_final: 0.6926 (t-90) REVERT: B 170 HIS cc_start: 0.8659 (p-80) cc_final: 0.8294 (p-80) REVERT: D 47 ARG cc_start: 0.6536 (mtt180) cc_final: 0.6311 (mtm-85) REVERT: E 116 GLU cc_start: 0.6870 (tt0) cc_final: 0.6591 (tt0) REVERT: E 145 GLU cc_start: 0.7349 (pp20) cc_final: 0.7081 (pp20) REVERT: F 96 VAL cc_start: 0.8140 (m) cc_final: 0.7508 (m) REVERT: H 114 ARG cc_start: 0.7947 (ttm-80) cc_final: 0.7674 (ttm170) REVERT: O 6 GLU cc_start: 0.8143 (mp0) cc_final: 0.7850 (mp0) REVERT: O 72 ARG cc_start: 0.6869 (ttp-110) cc_final: 0.6655 (ttm110) REVERT: Q 9 GLN cc_start: 0.8117 (mt0) cc_final: 0.7849 (mt0) REVERT: Q 43 LYS cc_start: 0.7529 (mtmt) cc_final: 0.7290 (mtpp) REVERT: R 50 LYS cc_start: 0.8749 (tttt) cc_final: 0.8200 (ttmm) REVERT: R 54 GLN cc_start: 0.7912 (mt0) cc_final: 0.7653 (mt0) REVERT: T 28 MET cc_start: 0.8072 (ttp) cc_final: 0.7750 (ptm) outliers start: 14 outliers final: 4 residues processed: 427 average time/residue: 0.6027 time to fit residues: 387.4525 Evaluate side-chains 299 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 295 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain F residue 36 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 6.9990 chunk 198 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 133 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 chunk 205 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 237 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 78 HIS ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 202 HIS B 19 GLN B 36 ASN B 120 GLN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN O 62 GLN P 18 GLN ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 3 ASN T 20 HIS ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 36963 Z= 0.371 Angle : 0.645 8.442 54707 Z= 0.328 Chirality : 0.040 0.226 6899 Planarity : 0.005 0.053 3369 Dihedral : 23.036 176.671 16988 Min Nonbonded Distance : 1.080 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.21 % Allowed : 10.47 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.66 (0.21), residues: 1702 helix: 1.41 (0.20), residues: 694 sheet: 0.10 (0.32), residues: 291 loop : -0.30 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 23 HIS 0.005 0.001 HIS E 89 PHE 0.018 0.002 PHE K 61 TYR 0.014 0.002 TYR L 66 ARG 0.007 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 308 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 23 GLN cc_start: 0.6761 (tp40) cc_final: 0.6513 (tp-100) REVERT: V 44 ILE cc_start: 0.6758 (mm) cc_final: 0.6370 (mt) REVERT: V 48 LEU cc_start: 0.8138 (tp) cc_final: 0.7850 (tt) REVERT: V 104 MET cc_start: 0.8064 (mmm) cc_final: 0.7676 (mmm) REVERT: V 142 LYS cc_start: 0.7585 (tppt) cc_final: 0.7348 (tppt) REVERT: V 257 TYR cc_start: 0.8531 (m-80) cc_final: 0.8327 (m-80) REVERT: B 168 HIS cc_start: 0.7396 (t-90) cc_final: 0.6720 (t-90) REVERT: D 47 ARG cc_start: 0.6882 (mtt180) cc_final: 0.6679 (mtm-85) REVERT: E 142 ASP cc_start: 0.6741 (m-30) cc_final: 0.6508 (m-30) REVERT: K 69 ARG cc_start: 0.7414 (mtm-85) cc_final: 0.6698 (mtt90) REVERT: T 39 ILE cc_start: 0.8932 (tp) cc_final: 0.8611 (mm) REVERT: T 79 LEU cc_start: 0.7960 (mt) cc_final: 0.7630 (mt) outliers start: 46 outliers final: 33 residues processed: 331 average time/residue: 0.5631 time to fit residues: 281.2742 Evaluate side-chains 306 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 273 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 25 VAL Chi-restraints excluded: chain V residue 199 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 10 MET Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 10 LYS Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain T residue 83 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 132 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 chunk 162 optimal weight: 0.5980 chunk 65 optimal weight: 7.9990 chunk 238 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 236 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 191 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 202 HIS B 36 ASN ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 HIS ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 109 ASN R 54 GLN ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN T 52 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 36963 Z= 0.194 Angle : 0.529 8.379 54707 Z= 0.274 Chirality : 0.034 0.220 6899 Planarity : 0.004 0.044 3369 Dihedral : 22.955 178.136 16988 Min Nonbonded Distance : 1.149 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.86 % Allowed : 12.71 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.86 (0.21), residues: 1702 helix: 1.63 (0.20), residues: 696 sheet: 0.16 (0.32), residues: 283 loop : -0.23 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 60 HIS 0.004 0.001 HIS E 89 PHE 0.010 0.001 PHE B 90 TYR 0.018 0.001 TYR V 157 ARG 0.006 0.001 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 298 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 23 GLN cc_start: 0.6697 (tp40) cc_final: 0.6477 (tp-100) REVERT: V 44 ILE cc_start: 0.6820 (mm) cc_final: 0.6418 (mt) REVERT: V 48 LEU cc_start: 0.8172 (tp) cc_final: 0.7865 (tt) REVERT: V 104 MET cc_start: 0.8289 (mmm) cc_final: 0.7865 (mmm) REVERT: B 96 TRP cc_start: 0.8247 (t-100) cc_final: 0.7844 (t-100) REVERT: B 168 HIS cc_start: 0.7372 (t-90) cc_final: 0.7065 (t-90) REVERT: Q 4 LYS cc_start: 0.6866 (tptm) cc_final: 0.6641 (tptp) REVERT: Q 5 ILE cc_start: 0.8584 (pt) cc_final: 0.8349 (pt) REVERT: Q 48 ASP cc_start: 0.7882 (t0) cc_final: 0.7610 (t70) REVERT: R 43 ARG cc_start: 0.7932 (ptt90) cc_final: 0.7723 (ptt90) REVERT: T 39 ILE cc_start: 0.8977 (tp) cc_final: 0.8413 (mm) REVERT: T 79 LEU cc_start: 0.8139 (mt) cc_final: 0.7830 (mt) outliers start: 41 outliers final: 32 residues processed: 322 average time/residue: 0.5392 time to fit residues: 265.4326 Evaluate side-chains 309 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 277 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 199 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain H residue 10 MET Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain R residue 42 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 235 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 239 optimal weight: 0.9990 chunk 253 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 226 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 202 HIS B 36 ASN B 120 GLN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 36963 Z= 0.234 Angle : 0.543 8.925 54707 Z= 0.281 Chirality : 0.035 0.224 6899 Planarity : 0.004 0.042 3369 Dihedral : 22.934 177.609 16988 Min Nonbonded Distance : 1.109 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.47 % Allowed : 12.08 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.21), residues: 1702 helix: 1.57 (0.20), residues: 695 sheet: 0.11 (0.32), residues: 283 loop : -0.32 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 23 HIS 0.005 0.001 HIS E 89 PHE 0.017 0.001 PHE K 61 TYR 0.032 0.002 TYR V 157 ARG 0.005 0.001 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 295 time to evaluate : 2.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 44 ILE cc_start: 0.6806 (mm) cc_final: 0.6408 (mt) REVERT: V 48 LEU cc_start: 0.8138 (tp) cc_final: 0.7828 (tt) REVERT: V 104 MET cc_start: 0.8233 (mmm) cc_final: 0.7871 (mmm) REVERT: V 142 LYS cc_start: 0.7581 (tppt) cc_final: 0.7294 (tppt) REVERT: V 157 TYR cc_start: 0.7692 (t80) cc_final: 0.7458 (t80) REVERT: B 96 TRP cc_start: 0.8268 (t-100) cc_final: 0.7864 (t-100) REVERT: B 168 HIS cc_start: 0.7409 (t-90) cc_final: 0.7041 (t-90) REVERT: E 148 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.7730 (p0) REVERT: K 94 GLU cc_start: 0.7540 (pp20) cc_final: 0.7123 (pp20) REVERT: O 6 GLU cc_start: 0.8312 (mp0) cc_final: 0.7959 (mp0) REVERT: Q 4 LYS cc_start: 0.6673 (tptm) cc_final: 0.6445 (tptp) REVERT: Q 5 ILE cc_start: 0.8692 (pt) cc_final: 0.8465 (pt) REVERT: Q 48 ASP cc_start: 0.8028 (t0) cc_final: 0.7728 (t70) REVERT: T 79 LEU cc_start: 0.8039 (mt) cc_final: 0.7762 (mt) outliers start: 64 outliers final: 50 residues processed: 326 average time/residue: 0.5359 time to fit residues: 267.9885 Evaluate side-chains 326 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 275 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 199 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain H residue 10 MET Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 56 ARG Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 75 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 188 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 216 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 227 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 202 HIS B 19 GLN B 36 ASN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 36963 Z= 0.293 Angle : 0.579 9.344 54707 Z= 0.299 Chirality : 0.037 0.236 6899 Planarity : 0.005 0.043 3369 Dihedral : 22.970 177.847 16988 Min Nonbonded Distance : 1.088 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.68 % Allowed : 13.69 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.57 (0.20), residues: 1702 helix: 1.41 (0.20), residues: 695 sheet: 0.07 (0.32), residues: 283 loop : -0.44 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 23 HIS 0.005 0.001 HIS E 89 PHE 0.011 0.002 PHE V 124 TYR 0.024 0.002 TYR V 157 ARG 0.005 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 278 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 48 LEU cc_start: 0.8088 (tp) cc_final: 0.7782 (tt) REVERT: V 104 MET cc_start: 0.8307 (mmm) cc_final: 0.7990 (mmm) REVERT: V 157 TYR cc_start: 0.7801 (t80) cc_final: 0.7513 (t80) REVERT: B 94 HIS cc_start: 0.6083 (m90) cc_final: 0.5845 (m170) REVERT: B 168 HIS cc_start: 0.7436 (t-90) cc_final: 0.7023 (t-90) REVERT: E 148 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7723 (p0) REVERT: F 13 ASP cc_start: 0.7318 (m-30) cc_final: 0.6676 (t0) REVERT: F 68 GLN cc_start: 0.7257 (mp10) cc_final: 0.7011 (mp10) REVERT: F 102 MET cc_start: 0.7060 (ppp) cc_final: 0.6795 (ppp) REVERT: O 6 GLU cc_start: 0.8271 (mp0) cc_final: 0.7920 (mp0) REVERT: O 88 ARG cc_start: 0.6986 (mmm160) cc_final: 0.6452 (mmp80) REVERT: Q 4 LYS cc_start: 0.6649 (tptm) cc_final: 0.6425 (tptp) REVERT: Q 48 ASP cc_start: 0.8143 (t0) cc_final: 0.7831 (t70) REVERT: T 39 ILE cc_start: 0.9165 (tp) cc_final: 0.8825 (mm) REVERT: T 79 LEU cc_start: 0.8063 (mt) cc_final: 0.7774 (mt) outliers start: 67 outliers final: 61 residues processed: 311 average time/residue: 0.5341 time to fit residues: 252.7870 Evaluate side-chains 332 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 270 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 25 VAL Chi-restraints excluded: chain V residue 199 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain H residue 10 MET Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 10 LYS Chi-restraints excluded: chain L residue 56 ARG Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 75 HIS Chi-restraints excluded: chain T residue 83 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 85 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 148 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 253 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 133 optimal weight: 20.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 202 HIS B 36 ASN ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 36963 Z= 0.286 Angle : 0.579 9.784 54707 Z= 0.299 Chirality : 0.037 0.229 6899 Planarity : 0.005 0.047 3369 Dihedral : 23.002 178.042 16988 Min Nonbonded Distance : 1.091 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.89 % Allowed : 14.59 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.51 (0.20), residues: 1702 helix: 1.41 (0.20), residues: 695 sheet: -0.03 (0.32), residues: 285 loop : -0.49 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 23 HIS 0.004 0.001 HIS E 89 PHE 0.011 0.001 PHE V 124 TYR 0.024 0.002 TYR V 157 ARG 0.006 0.001 ARG K 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 281 time to evaluate : 2.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 48 LEU cc_start: 0.8234 (tp) cc_final: 0.7852 (tt) REVERT: V 104 MET cc_start: 0.8302 (mmm) cc_final: 0.8048 (mmm) REVERT: V 142 LYS cc_start: 0.7554 (tppt) cc_final: 0.7252 (tppt) REVERT: V 157 TYR cc_start: 0.7814 (t80) cc_final: 0.7557 (t80) REVERT: B 90 PHE cc_start: 0.6071 (OUTLIER) cc_final: 0.5802 (m-10) REVERT: B 168 HIS cc_start: 0.7455 (t-90) cc_final: 0.7006 (t-90) REVERT: F 13 ASP cc_start: 0.7444 (m-30) cc_final: 0.6875 (t0) REVERT: F 102 MET cc_start: 0.7065 (ppp) cc_final: 0.6589 (ppp) REVERT: O 14 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7221 (mt-10) REVERT: O 88 ARG cc_start: 0.6911 (mmm160) cc_final: 0.6402 (mmp80) REVERT: Q 48 ASP cc_start: 0.8108 (t0) cc_final: 0.7793 (t70) REVERT: T 39 ILE cc_start: 0.9207 (tp) cc_final: 0.8847 (mm) REVERT: T 79 LEU cc_start: 0.7956 (mt) cc_final: 0.7639 (mt) outliers start: 70 outliers final: 61 residues processed: 318 average time/residue: 0.5327 time to fit residues: 260.1321 Evaluate side-chains 333 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 271 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 25 VAL Chi-restraints excluded: chain V residue 199 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain H residue 10 MET Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 56 ARG Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 75 HIS Chi-restraints excluded: chain T residue 83 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 244 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 213 optimal weight: 0.0020 chunk 141 optimal weight: 5.9990 chunk 252 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 202 HIS B 120 GLN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 ASN ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 36963 Z= 0.167 Angle : 0.517 10.211 54707 Z= 0.269 Chirality : 0.033 0.221 6899 Planarity : 0.004 0.041 3369 Dihedral : 22.934 178.348 16988 Min Nonbonded Distance : 1.136 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.56 % Allowed : 16.55 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.78 (0.21), residues: 1702 helix: 1.63 (0.20), residues: 696 sheet: 0.07 (0.32), residues: 285 loop : -0.34 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 60 HIS 0.004 0.001 HIS E 89 PHE 0.010 0.001 PHE K 105 TYR 0.022 0.001 TYR V 157 ARG 0.007 0.000 ARG K 56 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 284 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 48 LEU cc_start: 0.8218 (tp) cc_final: 0.7832 (tt) REVERT: V 142 LYS cc_start: 0.7446 (tppt) cc_final: 0.7184 (tppt) REVERT: V 157 TYR cc_start: 0.7870 (t80) cc_final: 0.7665 (t80) REVERT: B 113 ARG cc_start: 0.8111 (tpp80) cc_final: 0.7219 (tpm170) REVERT: B 168 HIS cc_start: 0.7415 (t-90) cc_final: 0.6923 (t-90) REVERT: F 13 ASP cc_start: 0.7534 (m-30) cc_final: 0.6941 (t0) REVERT: K 94 GLU cc_start: 0.7678 (pp20) cc_final: 0.7203 (pp20) REVERT: O 88 ARG cc_start: 0.6884 (mmm160) cc_final: 0.6388 (mmp80) REVERT: Q 48 ASP cc_start: 0.7920 (t0) cc_final: 0.7591 (t70) REVERT: T 39 ILE cc_start: 0.9192 (tp) cc_final: 0.8804 (mm) REVERT: T 79 LEU cc_start: 0.8063 (mt) cc_final: 0.7766 (mt) outliers start: 51 outliers final: 41 residues processed: 312 average time/residue: 0.5334 time to fit residues: 256.7563 Evaluate side-chains 313 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 272 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 199 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 75 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 156 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 172 optimal weight: 8.9990 chunk 124 optimal weight: 0.0770 chunk 23 optimal weight: 8.9990 chunk 198 optimal weight: 3.9990 overall best weight: 2.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 202 HIS B 120 GLN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 HIS ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 36963 Z= 0.253 Angle : 0.560 10.326 54707 Z= 0.289 Chirality : 0.036 0.229 6899 Planarity : 0.004 0.041 3369 Dihedral : 22.926 178.185 16988 Min Nonbonded Distance : 1.104 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.77 % Allowed : 16.90 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.60 (0.21), residues: 1702 helix: 1.48 (0.20), residues: 695 sheet: 0.02 (0.32), residues: 285 loop : -0.44 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 23 HIS 0.005 0.001 HIS E 89 PHE 0.022 0.001 PHE K 61 TYR 0.020 0.002 TYR V 157 ARG 0.007 0.001 ARG O 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 272 time to evaluate : 2.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 41 MET cc_start: 0.6736 (mtp) cc_final: 0.6509 (mtt) REVERT: V 48 LEU cc_start: 0.8164 (tp) cc_final: 0.7815 (tt) REVERT: B 113 ARG cc_start: 0.8125 (tpp80) cc_final: 0.7253 (ttm110) REVERT: B 168 HIS cc_start: 0.7431 (t-90) cc_final: 0.6940 (t-90) REVERT: B 191 SER cc_start: 0.8395 (m) cc_final: 0.7962 (m) REVERT: F 14 GLN cc_start: 0.7425 (pt0) cc_final: 0.7025 (pt0) REVERT: O 88 ARG cc_start: 0.6905 (mmm160) cc_final: 0.6398 (mmp80) REVERT: Q 48 ASP cc_start: 0.8029 (t0) cc_final: 0.7708 (t70) REVERT: T 39 ILE cc_start: 0.8968 (tp) cc_final: 0.8609 (mm) REVERT: T 79 LEU cc_start: 0.8050 (mt) cc_final: 0.7752 (mt) outliers start: 54 outliers final: 49 residues processed: 303 average time/residue: 0.5229 time to fit residues: 245.2182 Evaluate side-chains 317 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 268 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 25 VAL Chi-restraints excluded: chain V residue 199 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 75 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 229 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 chunk 220 optimal weight: 4.9990 chunk 235 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 212 optimal weight: 0.8980 chunk 222 optimal weight: 3.9990 chunk 234 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 202 HIS B 120 GLN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 HIS L 20 ASN ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 36963 Z= 0.234 Angle : 0.556 11.232 54707 Z= 0.288 Chirality : 0.035 0.226 6899 Planarity : 0.004 0.041 3369 Dihedral : 22.933 178.239 16988 Min Nonbonded Distance : 1.107 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.84 % Allowed : 17.04 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.53 (0.21), residues: 1702 helix: 1.42 (0.20), residues: 695 sheet: -0.06 (0.32), residues: 280 loop : -0.44 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 23 HIS 0.004 0.001 HIS E 89 PHE 0.022 0.001 PHE K 61 TYR 0.023 0.002 TYR V 157 ARG 0.006 0.000 ARG O 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 278 time to evaluate : 2.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 41 MET cc_start: 0.6748 (mtp) cc_final: 0.6512 (mtt) REVERT: V 48 LEU cc_start: 0.8175 (tp) cc_final: 0.7825 (tt) REVERT: V 142 LYS cc_start: 0.7493 (tppt) cc_final: 0.7229 (tppt) REVERT: B 113 ARG cc_start: 0.8220 (tpp80) cc_final: 0.7267 (ttm110) REVERT: B 168 HIS cc_start: 0.7435 (t-90) cc_final: 0.6938 (t-90) REVERT: B 191 SER cc_start: 0.8367 (m) cc_final: 0.7930 (m) REVERT: E 163 GLU cc_start: 0.7402 (pt0) cc_final: 0.7052 (pt0) REVERT: F 102 MET cc_start: 0.7195 (ppp) cc_final: 0.6995 (ppp) REVERT: K 94 GLU cc_start: 0.7724 (pp20) cc_final: 0.7207 (pp20) REVERT: O 88 ARG cc_start: 0.6890 (mmm160) cc_final: 0.6392 (mmp80) REVERT: Q 48 ASP cc_start: 0.8006 (t0) cc_final: 0.7681 (t70) REVERT: T 39 ILE cc_start: 0.8874 (tp) cc_final: 0.8582 (mm) REVERT: T 79 LEU cc_start: 0.8031 (mt) cc_final: 0.7722 (mt) outliers start: 55 outliers final: 51 residues processed: 309 average time/residue: 0.5268 time to fit residues: 250.4401 Evaluate side-chains 322 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 271 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 199 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 56 ARG Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 75 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 154 optimal weight: 8.9990 chunk 248 optimal weight: 0.4980 chunk 151 optimal weight: 0.0070 chunk 118 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 261 optimal weight: 0.9990 chunk 240 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 HIS ** H 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 36963 Z= 0.135 Angle : 0.509 10.929 54707 Z= 0.264 Chirality : 0.032 0.228 6899 Planarity : 0.004 0.038 3369 Dihedral : 22.827 178.727 16988 Min Nonbonded Distance : 1.169 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.72 % Allowed : 18.02 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.72 (0.21), residues: 1702 helix: 1.57 (0.20), residues: 703 sheet: 0.02 (0.33), residues: 261 loop : -0.35 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 60 HIS 0.003 0.000 HIS F 11 PHE 0.023 0.001 PHE K 61 TYR 0.015 0.001 TYR V 263 ARG 0.007 0.000 ARG O 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 295 time to evaluate : 2.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 142 LYS cc_start: 0.7389 (tppt) cc_final: 0.7108 (tppt) REVERT: V 157 TYR cc_start: 0.7818 (t80) cc_final: 0.7394 (t80) REVERT: B 94 HIS cc_start: 0.6386 (m90) cc_final: 0.6023 (m-70) REVERT: B 168 HIS cc_start: 0.7387 (t-90) cc_final: 0.6863 (t-90) REVERT: B 191 SER cc_start: 0.8291 (m) cc_final: 0.7912 (m) REVERT: F 102 MET cc_start: 0.7126 (ppp) cc_final: 0.6898 (ppp) REVERT: K 85 MET cc_start: 0.6796 (mmm) cc_final: 0.6457 (mmp) REVERT: K 94 GLU cc_start: 0.7610 (pp20) cc_final: 0.7083 (pp20) REVERT: O 88 ARG cc_start: 0.6880 (mmm160) cc_final: 0.6393 (mmp80) REVERT: Q 4 LYS cc_start: 0.6756 (tptm) cc_final: 0.6455 (tptp) REVERT: Q 48 ASP cc_start: 0.7845 (t0) cc_final: 0.7508 (t70) REVERT: T 39 ILE cc_start: 0.9130 (tp) cc_final: 0.8734 (mm) REVERT: T 79 LEU cc_start: 0.7869 (mt) cc_final: 0.7528 (mt) outliers start: 39 outliers final: 35 residues processed: 319 average time/residue: 0.5270 time to fit residues: 261.6806 Evaluate side-chains 316 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 281 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 199 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 56 ARG Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 75 HIS Chi-restraints excluded: chain T residue 86 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 165 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 191 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 208 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 213 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 HIS ** Q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.062853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.049762 restraints weight = 141647.967| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.49 r_work: 0.2898 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 36963 Z= 0.384 Angle : 0.655 11.175 54707 Z= 0.334 Chirality : 0.040 0.241 6899 Planarity : 0.005 0.050 3369 Dihedral : 22.996 177.853 16986 Min Nonbonded Distance : 1.075 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.00 % Allowed : 17.88 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.33 (0.21), residues: 1702 helix: 1.26 (0.20), residues: 695 sheet: -0.05 (0.32), residues: 272 loop : -0.62 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 23 HIS 0.005 0.001 HIS E 89 PHE 0.014 0.002 PHE V 124 TYR 0.017 0.002 TYR O 78 ARG 0.008 0.001 ARG F 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6947.94 seconds wall clock time: 126 minutes 47.72 seconds (7607.72 seconds total)