Starting phenix.real_space_refine on Wed Apr 10 04:20:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0n_35906/04_2024/8j0n_35906.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0n_35906/04_2024/8j0n_35906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0n_35906/04_2024/8j0n_35906.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0n_35906/04_2024/8j0n_35906.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0n_35906/04_2024/8j0n_35906.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0n_35906/04_2024/8j0n_35906.pdb" } resolution = 3.47 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= 0.034 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: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 11829 2.51 5 N 3152 2.21 5 O 3406 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 24": "OE1" <-> "OE2" Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A ASP 96": "OD1" <-> "OD2" Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 253": "OE1" <-> "OE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 528": "OD1" <-> "OD2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 675": "OD1" <-> "OD2" Residue "A TYR 684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 697": "OE1" <-> "OE2" Residue "A PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 804": "OE1" <-> "OE2" Residue "A PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 848": "OE1" <-> "OE2" Residue "A TYR 938": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 958": "OD1" <-> "OD2" Residue "B ASP 9": "OD1" <-> "OD2" Residue "B GLU 14": "OE1" <-> "OE2" Residue "B GLU 25": "OE1" <-> "OE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B GLU 38": "OE1" <-> "OE2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B ASP 104": "OD1" <-> "OD2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B GLU 143": "OE1" <-> "OE2" Residue "B TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "B GLU 179": "OE1" <-> "OE2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 5": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C ASP 51": "OD1" <-> "OD2" Residue "C TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 85": "OD1" <-> "OD2" Residue "C PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 157": "OE1" <-> "OE2" Residue "C ASP 162": "OD1" <-> "OD2" Residue "C TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 221": "OE1" <-> "OE2" Residue "C ASP 236": "OD1" <-> "OD2" Residue "C GLU 240": "OE1" <-> "OE2" Residue "C ASP 245": "OD1" <-> "OD2" Residue "C PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "E TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 69": "OD1" <-> "OD2" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 43": "OD1" <-> "OD2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "H ASP 56": "OD1" <-> "OD2" Residue "H PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 72": "OE1" <-> "OE2" Residue "H GLU 97": "OE1" <-> "OE2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "H ASP 128": "OD1" <-> "OD2" Residue "H GLU 181": "OE1" <-> "OE2" Residue "J GLU 57": "OE1" <-> "OE2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "J PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 92": "OE1" <-> "OE2" Residue "J GLU 139": "OE1" <-> "OE2" Residue "J GLU 174": "OE1" <-> "OE2" Residue "J GLU 203": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 18475 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7544 Classifications: {'peptide': 949} Link IDs: {'PTRANS': 43, 'TRANS': 905} Chain breaks: 2 Chain: "B" Number of atoms: 2438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2438 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 4, 'TRANS': 291} Chain: "C" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1976 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain breaks: 1 Chain: "D" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1222 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 10, 'TRANS': 145} Chain breaks: 1 Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 817 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "F" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 781 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "G" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 9, 'TRANS': 100} Chain: "H" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1559 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 8, 'TRANS': 186} Chain breaks: 1 Chain: "J" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1146 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 7, 'TRANS': 141} Chain breaks: 1 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 9.40, per 1000 atoms: 0.51 Number of scatterers: 18475 At special positions: 0 Unit cell: (131.89, 212.55, 113.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 3406 8.00 N 3152 7.00 C 11829 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 Links applied BETA1-4 " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG L 1 " - " ASN A 818 " " NAG M 1 " - " ASN A 913 " " NAG N 1 " - " ASN J 182 " Time building additional restraints: 7.25 Conformation dependent library (CDL) restraints added in 3.5 seconds 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4328 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 26 sheets defined 39.9% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 479 through 510 Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 655 through 666 Processing helix chain 'A' and resid 887 through 894 removed outlier: 3.628A pdb=" N ASN A 894 " --> pdb=" O SER A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 993 removed outlier: 3.908A pdb=" N ILE A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG A 981 " --> pdb=" O MET A 977 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 9 removed outlier: 3.511A pdb=" N ASP B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 26 Processing helix chain 'B' and resid 29 through 44 removed outlier: 4.199A pdb=" N GLU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 67 removed outlier: 3.828A pdb=" N ILE B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 83 Processing helix chain 'B' and resid 86 through 101 Processing helix chain 'B' and resid 102 through 117 removed outlier: 3.873A pdb=" N ALA B 106 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 135 removed outlier: 3.595A pdb=" N ARG B 124 " --> pdb=" O ASN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 152 removed outlier: 3.827A pdb=" N ALA B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 168 removed outlier: 3.519A pdb=" N TRP B 158 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 185 removed outlier: 3.586A pdb=" N PHE B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 203 removed outlier: 3.668A pdb=" N CYS B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY B 203 " --> pdb=" O LYS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 223 removed outlier: 3.571A pdb=" N LYS B 220 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 242 Processing helix chain 'B' and resid 246 through 270 Processing helix chain 'B' and resid 277 through 297 removed outlier: 3.909A pdb=" N SER B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 39 removed outlier: 3.535A pdb=" N VAL C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Proline residue: C 19 - end of helix Processing helix chain 'C' and resid 45 through 64 Processing helix chain 'C' and resid 69 through 82 Processing helix chain 'C' and resid 86 through 91 removed outlier: 3.858A pdb=" N LYS C 90 " --> pdb=" O GLY C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 132 removed outlier: 3.660A pdb=" N MET C 121 " --> pdb=" O ASN C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 148 through 153 Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.843A pdb=" N PHE C 177 " --> pdb=" O PHE C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 187 removed outlier: 4.209A pdb=" N SER C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE C 186 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 209 removed outlier: 3.748A pdb=" N MET C 198 " --> pdb=" O ASP C 194 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N MET C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 228 Processing helix chain 'C' and resid 237 through 242 removed outlier: 3.711A pdb=" N LEU C 241 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET C 242 " --> pdb=" O GLU C 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 237 through 242' Processing helix chain 'C' and resid 246 through 257 removed outlier: 3.645A pdb=" N GLY C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE C 252 " --> pdb=" O PHE C 248 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU C 255 " --> pdb=" O MET C 251 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU C 256 " --> pdb=" O PHE C 252 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN C 257 " --> pdb=" O LYS C 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 16 Processing helix chain 'D' and resid 61 through 73 removed outlier: 3.984A pdb=" N VAL D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA D 73 " --> pdb=" O CYS D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 79 Processing helix chain 'D' and resid 80 through 91 Processing helix chain 'D' and resid 95 through 113 Proline residue: D 109 - end of helix Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.751A pdb=" N THR D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 155 removed outlier: 3.562A pdb=" N PHE D 130 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU D 131 " --> pdb=" O SER D 127 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU D 134 " --> pdb=" O PHE D 130 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN D 140 " --> pdb=" O TYR D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 166 removed outlier: 3.523A pdb=" N TRP D 164 " --> pdb=" O HIS D 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 34 removed outlier: 3.505A pdb=" N LEU E 33 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR E 34 " --> pdb=" O TYR E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 64 removed outlier: 3.568A pdb=" N VAL E 46 " --> pdb=" O PRO E 42 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY E 59 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL E 61 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS E 62 " --> pdb=" O TYR E 58 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA E 64 " --> pdb=" O ILE E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 86 removed outlier: 3.671A pdb=" N LEU E 84 " --> pdb=" O THR E 80 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASN E 86 " --> pdb=" O ASP E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 101 removed outlier: 3.931A pdb=" N VAL E 99 " --> pdb=" O HIS E 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 45 removed outlier: 3.528A pdb=" N VAL F 19 " --> pdb=" O SER F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 71 removed outlier: 3.511A pdb=" N ALA F 70 " --> pdb=" O LEU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 78 removed outlier: 3.993A pdb=" N TYR F 77 " --> pdb=" O ARG F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 86 Processing helix chain 'F' and resid 90 through 108 removed outlier: 3.671A pdb=" N LEU F 98 " --> pdb=" O PHE F 94 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE F 99 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU F 103 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET F 106 " --> pdb=" O PHE F 102 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 63 removed outlier: 3.671A pdb=" N SER G 63 " --> pdb=" O GLN G 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 21 removed outlier: 3.624A pdb=" N TYR H 21 " --> pdb=" O HIS H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 83 removed outlier: 3.685A pdb=" N LEU H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 119 removed outlier: 3.997A pdb=" N GLY H 118 " --> pdb=" O ARG H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 177 Processing helix chain 'H' and resid 185 through 192 Processing helix chain 'H' and resid 199 through 210 Processing helix chain 'J' and resid 91 through 104 Processing helix chain 'J' and resid 133 through 140 removed outlier: 4.072A pdb=" N LEU J 137 " --> pdb=" O PRO J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 207 removed outlier: 3.675A pdb=" N PHE J 201 " --> pdb=" O GLU J 197 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.523A pdb=" N CYS A 933 " --> pdb=" O VAL A 947 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 44 removed outlier: 3.639A pdb=" N SER A 44 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL A 55 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL A 62 " --> pdb=" O THR A 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.598A pdb=" N THR A 99 " --> pdb=" O ARG A 108 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 108 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N MET A 107 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU A 120 " --> pdb=" O MET A 107 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER A 109 " --> pdb=" O ASN A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 135 removed outlier: 4.040A pdb=" N TRP A 163 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N HIS A 155 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LEU A 161 " --> pdb=" O HIS A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 179 through 180 removed outlier: 3.654A pdb=" N LYS A 201 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLN A 211 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ASN A 203 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE A 209 " --> pdb=" O ASN A 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 228 through 230 removed outlier: 3.901A pdb=" N GLY A 228 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 236 " --> pdb=" O GLY A 228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 275 through 278 removed outlier: 3.809A pdb=" N ARG A 275 " --> pdb=" O HIS A 294 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 292 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 291 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 303 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 293 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 301 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU A 302 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 313 " --> pdb=" O LEU A 302 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 321 through 326 Processing sheet with id=AA9, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 405 through 412 removed outlier: 3.505A pdb=" N GLY A 418 " --> pdb=" O PHE A 410 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 412 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 430 through 433 removed outlier: 4.351A pdb=" N TRP A 443 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 458 removed outlier: 3.932A pdb=" N CYS A 454 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS A 544 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU A 545 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS A 558 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY A 547 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 569 through 574 Processing sheet with id=AB5, first strand: chain 'A' and resid 625 through 633 removed outlier: 3.501A pdb=" N GLN A 625 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 641 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL A 639 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL A 631 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA A 637 " --> pdb=" O VAL A 631 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 692 through 699 removed outlier: 5.846A pdb=" N LEU A 694 " --> pdb=" O ARG A 685 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ARG A 685 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TRP A 696 " --> pdb=" O GLY A 683 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS A 682 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHE A 670 " --> pdb=" O GLY D 178 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLY D 180 " --> pdb=" O PHE A 670 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TYR A 672 " --> pdb=" O GLY D 180 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 705 through 711 removed outlier: 7.047A pdb=" N VAL A 744 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL A 710 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA A 742 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE A 757 " --> pdb=" O GLN A 775 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS A 771 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR J 191 " --> pdb=" O SER A 772 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 723 through 725 Processing sheet with id=AB9, first strand: chain 'A' and resid 778 through 786 removed outlier: 5.080A pdb=" N TRP A 796 " --> pdb=" O PRO A 781 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG A 802 " --> pdb=" O ASN A 797 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 821 through 822 removed outlier: 3.578A pdb=" N PHE A 822 " --> pdb=" O GLU D 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 847 through 849 Processing sheet with id=AC3, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.849A pdb=" N THR C 138 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 84 through 89 removed outlier: 3.779A pdb=" N ASP G 88 " --> pdb=" O PHE G 45 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE G 45 " --> pdb=" O ASP G 88 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU G 138 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET G 140 " --> pdb=" O ARG G 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 75 through 77 removed outlier: 3.558A pdb=" N ARG G 66 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY G 92 " --> pdb=" O ILE G 112 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 3 through 6 removed outlier: 6.857A pdb=" N GLY H 3 " --> pdb=" O THR H 52 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N PHE H 54 " --> pdb=" O GLY H 3 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LYS H 5 " --> pdb=" O PHE H 54 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ASP H 56 " --> pdb=" O LYS H 5 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL H 31 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N CYS H 57 " --> pdb=" O LEU H 29 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU H 29 " --> pdb=" O CYS H 57 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASN H 27 " --> pdb=" O PRO H 59 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N PHE H 61 " --> pdb=" O ALA H 25 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ALA H 25 " --> pdb=" O PHE H 61 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL H 26 " --> pdb=" O ALA H 95 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY H 91 " --> pdb=" O LEU H 30 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ALA H 32 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE H 89 " --> pdb=" O ALA H 32 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA H 123 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR H 92 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE H 125 " --> pdb=" O TYR H 92 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL H 127 " --> pdb=" O GLN H 94 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS H 153 " --> pdb=" O GLU H 145 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 83 through 87 removed outlier: 6.106A pdb=" N LYS J 70 " --> pdb=" O HIS J 58 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N HIS J 58 " --> pdb=" O LYS J 70 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY J 72 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU J 56 " --> pdb=" O GLY J 72 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU J 55 " --> pdb=" O PRO J 113 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG J 109 " --> pdb=" O SER J 59 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL J 128 " --> pdb=" O ILE J 112 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 156 through 162 removed outlier: 6.746A pdb=" N HIS J 149 " --> pdb=" O VAL J 157 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL J 159 " --> pdb=" O THR J 147 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR J 147 " --> pdb=" O VAL J 159 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL J 161 " --> pdb=" O GLN J 145 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLN J 145 " --> pdb=" O VAL J 161 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL J 150 " --> pdb=" O GLN J 188 " (cutoff:3.500A) 820 hydrogen bonds defined for protein. 2397 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.10 Time building geometry restraints manager: 7.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 1 1.04 - 1.23: 356 1.23 - 1.43: 7585 1.43 - 1.62: 10795 1.62 - 1.82: 153 Bond restraints: 18890 Sorted by residual: bond pdb=" CG PRO A 582 " pdb=" CD PRO A 582 " ideal model delta sigma weight residual 1.503 0.841 0.662 3.40e-02 8.65e+02 3.79e+02 bond pdb=" N PRO A 582 " pdb=" CD PRO A 582 " ideal model delta sigma weight residual 1.473 1.592 -0.119 1.40e-02 5.10e+03 7.24e+01 bond pdb=" CB PRO A 582 " pdb=" CG PRO A 582 " ideal model delta sigma weight residual 1.492 1.797 -0.305 5.00e-02 4.00e+02 3.72e+01 bond pdb=" CA LEU A 690 " pdb=" CB LEU A 690 " ideal model delta sigma weight residual 1.521 1.598 -0.077 1.48e-02 4.57e+03 2.73e+01 bond pdb=" CB PRO E 103 " pdb=" CG PRO E 103 " ideal model delta sigma weight residual 1.492 1.671 -0.179 5.00e-02 4.00e+02 1.28e+01 ... (remaining 18885 not shown) Histogram of bond angle deviations from ideal: 76.74 - 88.24: 2 88.24 - 99.73: 17 99.73 - 111.23: 8036 111.23 - 122.72: 15479 122.72 - 134.22: 2057 Bond angle restraints: 25591 Sorted by residual: angle pdb=" N PRO A 582 " pdb=" CD PRO A 582 " pdb=" CG PRO A 582 " ideal model delta sigma weight residual 103.20 76.74 26.46 1.50e+00 4.44e-01 3.11e+02 angle pdb=" CA PRO C 69 " pdb=" N PRO C 69 " pdb=" CD PRO C 69 " ideal model delta sigma weight residual 112.00 95.66 16.34 1.40e+00 5.10e-01 1.36e+02 angle pdb=" CA PRO E 103 " pdb=" N PRO E 103 " pdb=" CD PRO E 103 " ideal model delta sigma weight residual 112.00 97.35 14.65 1.40e+00 5.10e-01 1.09e+02 angle pdb=" CA PRO A 582 " pdb=" N PRO A 582 " pdb=" CD PRO A 582 " ideal model delta sigma weight residual 112.00 97.77 14.23 1.40e+00 5.10e-01 1.03e+02 angle pdb=" N PRO A 582 " pdb=" CA PRO A 582 " pdb=" CB PRO A 582 " ideal model delta sigma weight residual 103.48 94.38 9.10 1.00e+00 1.00e+00 8.28e+01 ... (remaining 25586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.59: 10034 21.59 - 43.19: 1131 43.19 - 64.78: 195 64.78 - 86.37: 45 86.37 - 107.96: 17 Dihedral angle restraints: 11422 sinusoidal: 4720 harmonic: 6702 Sorted by residual: dihedral pdb=" CA LEU A 929 " pdb=" C LEU A 929 " pdb=" N GLU A 930 " pdb=" CA GLU A 930 " ideal model delta harmonic sigma weight residual 180.00 147.11 32.89 0 5.00e+00 4.00e-02 4.33e+01 dihedral pdb=" CA MET C 151 " pdb=" C MET C 151 " pdb=" N LEU C 152 " pdb=" CA LEU C 152 " ideal model delta harmonic sigma weight residual -180.00 -154.59 -25.41 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA GLY B 67 " pdb=" C GLY B 67 " pdb=" N ARG B 68 " pdb=" CA ARG B 68 " ideal model delta harmonic sigma weight residual -180.00 -156.62 -23.38 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 11419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2625 0.078 - 0.157: 256 0.157 - 0.235: 1 0.235 - 0.314: 5 0.314 - 0.392: 2 Chirality restraints: 2889 Sorted by residual: chirality pdb=" CA PRO A 582 " pdb=" N PRO A 582 " pdb=" C PRO A 582 " pdb=" CB PRO A 582 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CA PRO E 103 " pdb=" N PRO E 103 " pdb=" C PRO E 103 " pdb=" CB PRO E 103 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2886 not shown) Planarity restraints: 3239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 68 " 0.110 5.00e-02 4.00e+02 1.52e-01 3.71e+01 pdb=" N PRO C 69 " -0.263 5.00e-02 4.00e+02 pdb=" CA PRO C 69 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO C 69 " 0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 581 " -0.098 5.00e-02 4.00e+02 1.34e-01 2.89e+01 pdb=" N PRO A 582 " 0.232 5.00e-02 4.00e+02 pdb=" CA PRO A 582 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO A 582 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 102 " 0.079 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO E 103 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO E 103 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 103 " 0.059 5.00e-02 4.00e+02 ... (remaining 3236 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 351 2.69 - 3.24: 16640 3.24 - 3.79: 27210 3.79 - 4.35: 33688 4.35 - 4.90: 56091 Nonbonded interactions: 133980 Sorted by model distance: nonbonded pdb=" OD1 ASP B 104 " pdb=" NE2 GLN B 108 " model vdw 2.136 2.520 nonbonded pdb=" OG1 THR H 52 " pdb=" OD2 ASP H 121 " model vdw 2.140 2.440 nonbonded pdb=" OG SER A 747 " pdb=" OD1 ASP A 749 " model vdw 2.176 2.440 nonbonded pdb=" NZ LYS H 20 " pdb=" O LEU H 183 " model vdw 2.282 2.520 nonbonded pdb=" OG SER A 787 " pdb=" N GLU A 788 " model vdw 2.292 2.520 ... (remaining 133975 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 2.770 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: 0.020 Extract box with map and model: 9.970 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 48.800 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.120 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2400 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 : 0.007 0.662 18890 Z= 0.416 Angle : 0.833 26.457 25591 Z= 0.463 Chirality : 0.044 0.392 2889 Planarity : 0.006 0.152 3236 Dihedral : 18.252 107.964 7094 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.23 % Favored : 91.50 % Rotamer: Outliers : 0.75 % Allowed : 28.06 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.17), residues: 2271 helix: 1.46 (0.19), residues: 836 sheet: 0.27 (0.24), residues: 444 loop : -3.25 (0.16), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 219 HIS 0.008 0.001 HIS A 306 PHE 0.019 0.001 PHE C 252 TYR 0.021 0.001 TYR A 305 ARG 0.010 0.000 ARG E 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 448 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 ILE cc_start: 0.4595 (mt) cc_final: 0.4198 (mt) REVERT: B 107 ILE cc_start: 0.4035 (mm) cc_final: 0.3611 (mm) REVERT: B 183 MET cc_start: 0.0394 (OUTLIER) cc_final: -0.0118 (mmt) REVERT: C 81 ASN cc_start: 0.4450 (m110) cc_final: 0.3554 (t0) REVERT: C 121 MET cc_start: 0.4674 (ppp) cc_final: 0.4261 (tpp) REVERT: C 232 TRP cc_start: 0.1901 (t60) cc_final: 0.1362 (t60) REVERT: E 31 MET cc_start: 0.6029 (tpt) cc_final: 0.5370 (ttt) REVERT: H 110 LYS cc_start: 0.5931 (mttt) cc_final: 0.5726 (tptp) outliers start: 15 outliers final: 2 residues processed: 460 average time/residue: 0.4048 time to fit residues: 258.3160 Evaluate side-chains 243 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 240 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain D residue 43 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 190 optimal weight: 7.9990 chunk 171 optimal weight: 0.0980 chunk 95 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 205 optimal weight: 0.0980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 661 GLN ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN B 120 ASN B 155 GLN B 188 ASN B 193 GLN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN H 9 GLN H 199 ASN ** J 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3116 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 18890 Z= 0.265 Angle : 0.796 12.119 25591 Z= 0.392 Chirality : 0.046 0.280 2889 Planarity : 0.006 0.069 3236 Dihedral : 6.909 59.109 2691 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.59 % Favored : 91.11 % Rotamer: Outliers : 5.74 % Allowed : 27.16 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.17), residues: 2271 helix: 1.34 (0.18), residues: 859 sheet: 0.32 (0.23), residues: 468 loop : -3.18 (0.16), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 151 HIS 0.010 0.002 HIS H 85 PHE 0.028 0.002 PHE B 230 TYR 0.025 0.002 TYR C 67 ARG 0.008 0.001 ARG A 891 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 275 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7309 (tmm) cc_final: 0.6926 (tmm) REVERT: A 174 HIS cc_start: 0.8341 (t-170) cc_final: 0.8085 (t70) REVERT: A 292 PHE cc_start: 0.6129 (m-80) cc_final: 0.5770 (m-10) REVERT: A 294 HIS cc_start: 0.4716 (t-170) cc_final: 0.4307 (t-170) REVERT: A 375 ILE cc_start: 0.6545 (mt) cc_final: 0.5483 (mt) REVERT: A 427 ASP cc_start: -0.1543 (OUTLIER) cc_final: -0.3386 (t0) REVERT: A 833 VAL cc_start: 0.6813 (t) cc_final: 0.6533 (p) REVERT: A 847 MET cc_start: 0.1483 (mmt) cc_final: 0.0751 (mtm) REVERT: B 32 GLN cc_start: 0.7187 (pp30) cc_final: 0.6942 (pp30) REVERT: B 64 LEU cc_start: 0.3343 (OUTLIER) cc_final: 0.2866 (tp) REVERT: C 36 ILE cc_start: 0.4874 (OUTLIER) cc_final: 0.4613 (mt) REVERT: C 121 MET cc_start: 0.5445 (ppp) cc_final: 0.5014 (tpp) REVERT: C 137 THR cc_start: 0.5334 (OUTLIER) cc_final: 0.5102 (m) REVERT: C 232 TRP cc_start: 0.2698 (t60) cc_final: 0.2375 (t60) REVERT: E 31 MET cc_start: 0.6169 (tpt) cc_final: 0.5611 (ttt) REVERT: H 133 THR cc_start: 0.1093 (OUTLIER) cc_final: 0.0693 (m) REVERT: H 166 GLU cc_start: 0.8015 (mp0) cc_final: 0.7768 (mm-30) REVERT: H 209 LEU cc_start: 0.3208 (OUTLIER) cc_final: 0.2846 (mt) REVERT: J 77 ASN cc_start: 0.5183 (t0) cc_final: 0.4975 (t0) REVERT: J 139 GLU cc_start: -0.0457 (OUTLIER) cc_final: -0.2709 (pp20) outliers start: 115 outliers final: 36 residues processed: 372 average time/residue: 0.3244 time to fit residues: 182.5908 Evaluate side-chains 272 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 229 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 139 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 114 optimal weight: 0.0370 chunk 63 optimal weight: 5.9990 chunk 170 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 205 optimal weight: 6.9990 chunk 222 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 203 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 ASN ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 HIS ** A 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 ASN B 32 GLN B 194 GLN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN H 199 ASN ** J 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3385 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18890 Z= 0.227 Angle : 0.752 13.186 25591 Z= 0.360 Chirality : 0.045 0.345 2889 Planarity : 0.005 0.065 3236 Dihedral : 5.542 58.886 2686 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.84 % Favored : 91.85 % Rotamer: Outliers : 4.74 % Allowed : 27.96 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.17), residues: 2271 helix: 1.49 (0.18), residues: 856 sheet: 0.35 (0.24), residues: 472 loop : -3.00 (0.17), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 163 HIS 0.013 0.001 HIS E 62 PHE 0.048 0.002 PHE B 230 TYR 0.029 0.002 TYR B 8 ARG 0.013 0.001 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 262 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 HIS cc_start: 0.8308 (t-170) cc_final: 0.8078 (t-90) REVERT: A 375 ILE cc_start: 0.6372 (mt) cc_final: 0.6057 (mt) REVERT: A 427 ASP cc_start: -0.1252 (OUTLIER) cc_final: -0.3485 (t0) REVERT: A 830 LEU cc_start: 0.6937 (mt) cc_final: 0.6488 (mt) REVERT: B 32 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.6822 (pp30) REVERT: B 64 LEU cc_start: 0.4036 (OUTLIER) cc_final: 0.3533 (tp) REVERT: B 181 LEU cc_start: 0.4308 (OUTLIER) cc_final: 0.4048 (mt) REVERT: B 183 MET cc_start: 0.0818 (mtt) cc_final: 0.0480 (mmt) REVERT: C 36 ILE cc_start: 0.4952 (OUTLIER) cc_final: 0.4684 (mt) REVERT: C 121 MET cc_start: 0.5729 (ppp) cc_final: 0.5206 (tpp) REVERT: C 208 MET cc_start: 0.6481 (ppp) cc_final: 0.6220 (ppp) REVERT: E 31 MET cc_start: 0.6223 (tpt) cc_final: 0.5634 (ttt) REVERT: J 77 ASN cc_start: 0.5612 (t0) cc_final: 0.5342 (t0) REVERT: J 139 GLU cc_start: -0.0370 (OUTLIER) cc_final: -0.2433 (pp20) outliers start: 95 outliers final: 40 residues processed: 343 average time/residue: 0.3124 time to fit residues: 162.2243 Evaluate side-chains 272 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 226 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 797 ASN Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 805 PHE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain J residue 147 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 203 optimal weight: 4.9990 chunk 154 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 206 optimal weight: 0.0570 chunk 218 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 195 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 167 ASN B 238 HIS C 71 GLN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN J 141 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3529 moved from start: 0.6190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18890 Z= 0.211 Angle : 0.735 10.540 25591 Z= 0.350 Chirality : 0.044 0.308 2889 Planarity : 0.005 0.063 3236 Dihedral : 4.959 58.546 2686 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.75 % Favored : 91.94 % Rotamer: Outliers : 4.79 % Allowed : 28.16 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.17), residues: 2271 helix: 1.45 (0.18), residues: 851 sheet: 0.38 (0.24), residues: 473 loop : -2.94 (0.17), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 232 HIS 0.021 0.001 HIS B 238 PHE 0.057 0.002 PHE B 230 TYR 0.031 0.002 TYR B 8 ARG 0.013 0.001 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 239 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 TRP cc_start: 0.7836 (m100) cc_final: 0.7197 (m100) REVERT: A 292 PHE cc_start: 0.6086 (m-80) cc_final: 0.5885 (m-10) REVERT: A 327 THR cc_start: 0.8122 (OUTLIER) cc_final: 0.7896 (t) REVERT: A 457 MET cc_start: 0.2663 (mmt) cc_final: 0.2277 (mmm) REVERT: A 687 ARG cc_start: 0.3886 (ttm-80) cc_final: 0.3663 (ttm-80) REVERT: A 853 GLU cc_start: 0.1661 (OUTLIER) cc_final: 0.1425 (mp0) REVERT: B 32 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.6924 (pp30) REVERT: B 64 LEU cc_start: 0.3953 (OUTLIER) cc_final: 0.3640 (tp) REVERT: B 183 MET cc_start: 0.0873 (mtt) cc_final: 0.0421 (mmt) REVERT: C 36 ILE cc_start: 0.5015 (OUTLIER) cc_final: 0.4750 (mt) REVERT: C 121 MET cc_start: 0.5842 (ppp) cc_final: 0.5275 (tpp) REVERT: E 31 MET cc_start: 0.6256 (tpt) cc_final: 0.5698 (ttt) REVERT: H 209 LEU cc_start: 0.3267 (OUTLIER) cc_final: 0.2886 (mt) REVERT: J 63 ASP cc_start: 0.7452 (p0) cc_final: 0.7203 (p0) REVERT: J 77 ASN cc_start: 0.5732 (t0) cc_final: 0.5494 (t0) outliers start: 96 outliers final: 54 residues processed: 313 average time/residue: 0.3057 time to fit residues: 146.9014 Evaluate side-chains 269 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 209 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 797 ASN Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 805 PHE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 177 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 181 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 186 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 196 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN A 559 GLN A 625 GLN ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 HIS A 775 GLN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 GLN A 836 GLN ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 GLN B 32 GLN B 42 ASN B 159 HIS C 195 GLN D 140 ASN G 124 ASN ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN H 105 ASN H 147 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3893 moved from start: 0.7267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18890 Z= 0.236 Angle : 0.734 11.077 25591 Z= 0.358 Chirality : 0.043 0.331 2889 Planarity : 0.005 0.063 3236 Dihedral : 4.841 58.651 2686 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.79 % Favored : 91.85 % Rotamer: Outliers : 5.09 % Allowed : 28.26 % Favored : 66.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.18), residues: 2271 helix: 1.51 (0.18), residues: 850 sheet: 0.45 (0.24), residues: 472 loop : -2.94 (0.17), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP C 232 HIS 0.008 0.001 HIS E 62 PHE 0.045 0.002 PHE B 230 TYR 0.024 0.002 TYR B 66 ARG 0.009 0.001 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 260 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 HIS cc_start: 0.8122 (t-90) cc_final: 0.7866 (t70) REVERT: A 209 ILE cc_start: 0.7972 (mt) cc_final: 0.7755 (tp) REVERT: A 291 PHE cc_start: 0.6511 (p90) cc_final: 0.6145 (p90) REVERT: A 303 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7250 (pp) REVERT: A 327 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.8228 (t) REVERT: A 373 TYR cc_start: 0.5838 (m-10) cc_final: 0.4280 (m-80) REVERT: A 531 ASN cc_start: 0.5876 (OUTLIER) cc_final: 0.4996 (p0) REVERT: A 687 ARG cc_start: 0.4083 (ttm-80) cc_final: 0.3870 (ttm-80) REVERT: A 853 GLU cc_start: 0.2055 (OUTLIER) cc_final: 0.1562 (mp0) REVERT: B 32 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.7082 (pp30) REVERT: B 183 MET cc_start: 0.1638 (mtt) cc_final: 0.1309 (ptt) REVERT: C 146 LEU cc_start: 0.0680 (OUTLIER) cc_final: 0.0063 (mp) REVERT: E 31 MET cc_start: 0.6406 (tpt) cc_final: 0.5814 (ttt) REVERT: G 124 ASN cc_start: 0.7184 (OUTLIER) cc_final: 0.6571 (t0) REVERT: H 110 LYS cc_start: 0.4069 (tptp) cc_final: 0.3418 (ttpt) REVERT: H 209 LEU cc_start: 0.3305 (OUTLIER) cc_final: 0.2845 (mt) REVERT: J 70 LYS cc_start: 0.4741 (tptp) cc_final: 0.3764 (tppt) REVERT: J 77 ASN cc_start: 0.5945 (t0) cc_final: 0.5670 (t0) outliers start: 102 outliers final: 60 residues processed: 343 average time/residue: 0.3017 time to fit residues: 159.4037 Evaluate side-chains 293 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 225 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 752 HIS Chi-restraints excluded: chain A residue 797 ASN Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 115 ARG Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 177 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 73 optimal weight: 6.9990 chunk 196 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 218 optimal weight: 0.3980 chunk 181 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 HIS ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN G 124 ASN ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN J 188 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4033 moved from start: 0.7871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18890 Z= 0.215 Angle : 0.741 11.297 25591 Z= 0.356 Chirality : 0.043 0.319 2889 Planarity : 0.005 0.091 3236 Dihedral : 4.817 59.148 2686 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.10 % Favored : 91.55 % Rotamer: Outliers : 4.44 % Allowed : 30.85 % Favored : 64.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.18), residues: 2271 helix: 1.52 (0.18), residues: 856 sheet: 0.50 (0.24), residues: 457 loop : -2.93 (0.17), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 232 HIS 0.017 0.001 HIS A 428 PHE 0.053 0.002 PHE B 230 TYR 0.038 0.002 TYR B 66 ARG 0.006 0.001 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 250 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ILE cc_start: 0.7797 (mt) cc_final: 0.7531 (tp) REVERT: A 291 PHE cc_start: 0.6584 (p90) cc_final: 0.6214 (p90) REVERT: A 303 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7273 (pp) REVERT: A 327 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8309 (t) REVERT: A 787 SER cc_start: 0.2270 (OUTLIER) cc_final: 0.1995 (t) REVERT: B 32 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7476 (tt0) REVERT: C 121 MET cc_start: 0.6799 (ttt) cc_final: 0.5671 (tpp) REVERT: E 31 MET cc_start: 0.6405 (tpt) cc_final: 0.5846 (ttt) REVERT: F 84 LEU cc_start: 0.3436 (mp) cc_final: 0.3145 (mm) REVERT: G 124 ASN cc_start: 0.7157 (OUTLIER) cc_final: 0.6641 (t0) REVERT: H 110 LYS cc_start: 0.4156 (tptp) cc_final: 0.3569 (ttpt) REVERT: H 134 MET cc_start: 0.3730 (pmm) cc_final: 0.3265 (pmm) REVERT: H 209 LEU cc_start: 0.3153 (OUTLIER) cc_final: 0.2715 (mt) REVERT: J 70 LYS cc_start: 0.4892 (tptp) cc_final: 0.3942 (tppt) REVERT: J 77 ASN cc_start: 0.6231 (t0) cc_final: 0.5948 (t0) REVERT: J 139 GLU cc_start: -0.0726 (OUTLIER) cc_final: -0.2642 (pp20) outliers start: 89 outliers final: 59 residues processed: 318 average time/residue: 0.3011 time to fit residues: 148.1184 Evaluate side-chains 292 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 226 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 752 HIS Chi-restraints excluded: chain A residue 787 SER Chi-restraints excluded: chain A residue 797 ASN Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain J residue 164 HIS Chi-restraints excluded: chain J residue 177 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 210 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 184 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 217 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 ASN ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN J 188 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4815 moved from start: 0.9999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 18890 Z= 0.360 Angle : 0.937 31.067 25591 Z= 0.466 Chirality : 0.050 0.538 2889 Planarity : 0.007 0.106 3236 Dihedral : 5.519 59.138 2686 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 23.95 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.54 % Favored : 91.06 % Rotamer: Outliers : 5.54 % Allowed : 30.00 % Favored : 64.45 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.17), residues: 2271 helix: 1.00 (0.18), residues: 855 sheet: 0.16 (0.24), residues: 455 loop : -3.17 (0.16), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 232 HIS 0.039 0.003 HIS A 583 PHE 0.050 0.003 PHE B 230 TYR 0.037 0.003 TYR E 30 ARG 0.011 0.001 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 290 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 MET cc_start: 0.4890 (mmm) cc_final: 0.4345 (mmt) REVERT: A 957 LYS cc_start: 0.7323 (tttt) cc_final: 0.7008 (ttpt) REVERT: B 32 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7709 (pp30) REVERT: B 33 ILE cc_start: 0.7051 (mt) cc_final: 0.6387 (mt) REVERT: B 215 PHE cc_start: 0.0064 (OUTLIER) cc_final: -0.0178 (t80) REVERT: C 51 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8046 (p0) REVERT: C 121 MET cc_start: 0.7333 (ttt) cc_final: 0.6997 (tpp) REVERT: E 31 MET cc_start: 0.6576 (tpt) cc_final: 0.5859 (ttt) REVERT: H 13 LYS cc_start: 0.6213 (mtmt) cc_final: 0.5614 (mtmt) REVERT: H 175 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6560 (pp) REVERT: H 209 LEU cc_start: 0.3208 (OUTLIER) cc_final: 0.2643 (mt) REVERT: J 77 ASN cc_start: 0.6482 (t0) cc_final: 0.6141 (t0) outliers start: 111 outliers final: 78 residues processed: 382 average time/residue: 0.2905 time to fit residues: 173.7869 Evaluate side-chains 341 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 258 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 797 ASN Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 173 SER Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 115 ARG Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 177 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 134 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 130 optimal weight: 0.0370 chunk 65 optimal weight: 0.0070 chunk 42 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 148 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 171 optimal weight: 0.5980 chunk 198 optimal weight: 0.5980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 HIS ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 GLN ** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 HIS ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN B 155 GLN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4738 moved from start: 1.0264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18890 Z= 0.204 Angle : 0.798 15.478 25591 Z= 0.377 Chirality : 0.045 0.328 2889 Planarity : 0.005 0.068 3236 Dihedral : 5.097 59.913 2686 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.75 % Favored : 91.90 % Rotamer: Outliers : 3.74 % Allowed : 33.45 % Favored : 62.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.17), residues: 2271 helix: 1.19 (0.18), residues: 859 sheet: 0.37 (0.24), residues: 456 loop : -3.15 (0.17), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 17 HIS 0.014 0.001 HIS A 428 PHE 0.057 0.002 PHE B 230 TYR 0.031 0.002 TYR B 66 ARG 0.013 0.001 ARG A 660 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 273 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6730 (mtt) cc_final: 0.5849 (mtt) REVERT: A 427 ASP cc_start: 0.0868 (OUTLIER) cc_final: -0.1494 (t0) REVERT: A 457 MET cc_start: 0.5551 (mmm) cc_final: 0.5005 (mmt) REVERT: A 536 MET cc_start: 0.5021 (ppp) cc_final: 0.4044 (ptm) REVERT: C 51 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8049 (p0) REVERT: C 121 MET cc_start: 0.7243 (ttt) cc_final: 0.6337 (tpp) REVERT: E 31 MET cc_start: 0.6757 (tpt) cc_final: 0.5806 (ttt) REVERT: E 96 ARG cc_start: 0.5248 (OUTLIER) cc_final: 0.4789 (ptm-80) REVERT: H 170 ILE cc_start: 0.6778 (tt) cc_final: 0.6460 (tp) REVERT: H 175 LEU cc_start: 0.6557 (OUTLIER) cc_final: 0.6235 (pp) REVERT: J 77 ASN cc_start: 0.6594 (t0) cc_final: 0.6244 (t0) outliers start: 75 outliers final: 56 residues processed: 332 average time/residue: 0.2864 time to fit residues: 148.7408 Evaluate side-chains 305 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 245 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 797 ASN Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 215 ASN Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 115 ARG Chi-restraints excluded: chain J residue 164 HIS Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 177 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 208 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 chunk 202 optimal weight: 0.4980 chunk 122 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 159 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 GLN ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5544 moved from start: 1.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.202 18890 Z= 0.384 Angle : 1.000 18.375 25591 Z= 0.496 Chirality : 0.053 0.462 2889 Planarity : 0.007 0.080 3236 Dihedral : 5.947 67.037 2686 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 27.36 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.51 % Favored : 90.09 % Rotamer: Outliers : 4.44 % Allowed : 33.65 % Favored : 61.91 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.17), residues: 2271 helix: 0.62 (0.18), residues: 853 sheet: -0.12 (0.23), residues: 464 loop : -3.17 (0.17), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 992 HIS 0.039 0.003 HIS A 196 PHE 0.076 0.004 PHE B 230 TYR 0.036 0.003 TYR E 30 ARG 0.011 0.001 ARG J 111 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 311 time to evaluate : 2.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 VAL cc_start: 0.7570 (OUTLIER) cc_final: 0.7301 (m) REVERT: A 457 MET cc_start: 0.6949 (mmm) cc_final: 0.6568 (mmt) REVERT: A 505 MET cc_start: 0.7575 (mmp) cc_final: 0.7328 (mmp) REVERT: A 535 MET cc_start: 0.5346 (OUTLIER) cc_final: 0.4801 (ttm) REVERT: A 660 ARG cc_start: 0.8389 (ptt-90) cc_final: 0.8167 (ptt-90) REVERT: B 36 VAL cc_start: 0.8445 (t) cc_final: 0.8047 (p) REVERT: B 167 ASN cc_start: 0.3531 (OUTLIER) cc_final: 0.3178 (p0) REVERT: C 51 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8213 (p0) REVERT: C 121 MET cc_start: 0.7864 (ttt) cc_final: 0.7441 (tpp) REVERT: D 120 PHE cc_start: 0.2804 (OUTLIER) cc_final: 0.1793 (m-80) REVERT: H 170 ILE cc_start: 0.7361 (tt) cc_final: 0.7048 (tp) REVERT: H 175 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6827 (pp) REVERT: H 203 ASN cc_start: 0.7960 (m110) cc_final: 0.7333 (p0) REVERT: J 77 ASN cc_start: 0.7087 (t0) cc_final: 0.6816 (t0) outliers start: 89 outliers final: 54 residues processed: 379 average time/residue: 0.2998 time to fit residues: 174.6583 Evaluate side-chains 326 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 266 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 62 HIS Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 97 ARG Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 177 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 131 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 225 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 142 optimal weight: 0.3980 chunk 190 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 HIS ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 GLN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 GLN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 ASN H 62 HIS H 189 HIS ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5525 moved from start: 1.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18890 Z= 0.233 Angle : 0.870 15.352 25591 Z= 0.414 Chirality : 0.046 0.271 2889 Planarity : 0.006 0.067 3236 Dihedral : 5.335 59.953 2684 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.15 % Favored : 91.46 % Rotamer: Outliers : 2.45 % Allowed : 36.25 % Favored : 61.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.17), residues: 2271 helix: 0.91 (0.18), residues: 850 sheet: 0.13 (0.23), residues: 468 loop : -3.13 (0.17), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 17 HIS 0.046 0.002 HIS A 222 PHE 0.056 0.002 PHE B 230 TYR 0.033 0.002 TYR E 30 ARG 0.016 0.001 ARG A 859 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 293 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 VAL cc_start: 0.7495 (OUTLIER) cc_final: 0.7279 (m) REVERT: A 930 GLU cc_start: 0.5289 (tp30) cc_final: 0.5012 (tp30) REVERT: A 954 ASP cc_start: 0.6845 (t0) cc_final: 0.6532 (t0) REVERT: C 51 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8164 (p0) REVERT: C 121 MET cc_start: 0.7910 (ttt) cc_final: 0.7494 (tpp) REVERT: D 120 PHE cc_start: 0.2790 (OUTLIER) cc_final: 0.1786 (m-80) REVERT: E 31 MET cc_start: 0.6836 (tpt) cc_final: 0.6435 (tpt) REVERT: H 170 ILE cc_start: 0.7356 (tt) cc_final: 0.6988 (tp) REVERT: H 175 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6840 (pp) REVERT: J 77 ASN cc_start: 0.7038 (t0) cc_final: 0.6826 (t0) outliers start: 49 outliers final: 39 residues processed: 331 average time/residue: 0.2787 time to fit residues: 144.4727 Evaluate side-chains 320 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 277 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 803 ASN Chi-restraints excluded: chain A residue 905 HIS Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 62 HIS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 177 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 54 optimal weight: 0.0470 chunk 165 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 179 optimal weight: 6.9990 chunk 75 optimal weight: 0.3980 chunk 184 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 GLN ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.095712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.077909 restraints weight = 85876.991| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 6.12 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 1.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18890 Z= 0.257 Angle : 0.881 15.516 25591 Z= 0.423 Chirality : 0.046 0.232 2889 Planarity : 0.006 0.064 3236 Dihedral : 5.397 58.269 2684 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.37 % Favored : 91.24 % Rotamer: Outliers : 2.95 % Allowed : 36.00 % Favored : 61.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.17), residues: 2271 helix: 0.93 (0.18), residues: 849 sheet: 0.28 (0.23), residues: 467 loop : -3.11 (0.17), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 110 HIS 0.016 0.002 HIS H 62 PHE 0.059 0.002 PHE B 230 TYR 0.038 0.002 TYR E 30 ARG 0.013 0.001 ARG A 859 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4394.41 seconds wall clock time: 80 minutes 43.55 seconds (4843.55 seconds total)